19-41302850-GGC-TCA

Variant names:

• chr19-41302850-GGC-TCA
• NM_007040.6:c.1873_1875delGGCinsTCA
• HNRNPUL1 p.Gly625Ser

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+2 Uncertain · Warm

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 2 classification points (ACMG Germline Pathogenicity v2019). PM2

The NM_007040.6(HNRNPUL1):c.1873_1875delGGCinsTCA (p.Gly625Ser) variant causes a missense change. Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.G625S: Uncertain_significance (ClinVar VariationId 4035778, 1 star)

• Frequency: Genomes: not found (cov: 31)
• Consequence: HNRNPUL1 NM_007040.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.38
• Publications: 0 publications found

Genes affected

HNRNPUL1 (HGNC:17011): (heterogeneous nuclear ribonucleoprotein U like 1) This gene encodes a nuclear RNA-binding protein of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. This protein binds specifically to adenovirus early-1B-55kDa oncoprotein. It may play an important role in nucleocytoplasmic RNA transport, and its function is modulated by early-1B-55kDa in adenovirus-infected cells. [provided by RefSeq, Mar 2016]

TGFB1 (HGNC:11766): (transforming growth factor beta 1) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate a latency-associated peptide (LAP) and a mature peptide, and is found in either a latent form composed of a mature peptide homodimer, a LAP homodimer, and a latent TGF-beta binding protein, or in an active form consisting solely of the mature peptide homodimer. The mature peptide may also form heterodimers with other TGFB family members. This encoded protein regulates cell proliferation, differentiation and growth, and can modulate expression and activation of other growth factors including interferon gamma and tumor necrosis factor alpha. This gene is frequently upregulated in tumor cells, and mutations in this gene result in Camurati-Engelmann disease. [provided by RefSeq, Aug 2016]

TGFB1 Gene-Disease associations (from GenCC):

• Camurati-Engelmann disease

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp, G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• Camurati-Engelmann disease type 1

  Inheritance: AD Classification: STRONG Submitted by: PanelApp Australia
• inflammatory bowel disease, immunodeficiency, and encephalopathy

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Orphanet, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
• cystic fibrosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: unknown) (threshold 0.001) — PM2 moderate.

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_007040.6. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	HNRNPUL1 NM_007040.6	MANE Select	c.1873_1875delGGCinsTCA p.Gly625Ser	missense	N/A	Prot: NP_008971.2
	HNRNPUL1 NM_001439168.1		c.1873_1875delGGCinsTCA p.Gly625Ser	missense	N/A	Prot: NP_001426097.1
	HNRNPUL1 NM_001439167.1		c.1873_1875delGGCinsTCA p.Gly625Ser	missense	N/A	Prot: NP_001426096.1 UniProt:

HNRNPUL1 NM_007040.6

MANE Select

HGVSc / HGVSpc.1873_1875delGGCinsTCAp.Gly625Ser

Exon rankN/A

missense

Prot: NP_008971.2

HNRNPUL1 NM_001439168.1

HGVSc / HGVSpc.1873_1875delGGCinsTCAp.Gly625Ser

Exon rankN/A

missense

Prot: NP_001426097.1

HNRNPUL1 NM_001439167.1

HGVSc / HGVSpc.1873_1875delGGCinsTCAp.Gly625Ser

Exon rankN/A

missense

Prot: NP_001426096.1UniProt: Q9BUJ2-2

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	HNRNPUL1 ENST00000392006.8	TSL:1MANE Select	c.1873_1875delGGCinsTCA p.Gly625Ser	missense	N/A	Prot: ENSP00000375863.2 UniProt:
	HNRNPUL1 ENST00000602130.5	TSL:1	c.1873_1875delGGCinsTCA p.Gly625Ser	missense	N/A	Prot: ENSP00000470687.1 UniProt:
	HNRNPUL1 ENST00000352456.7	TSL:1	c.1573_1575delGGCinsTCA p.Gly525Ser	missense	N/A	Prot: ENSP00000340857.3 UniProt:

HNRNPUL1 ENST00000392006.8

TSL:1MANE Select

HGVSc / HGVSpc.1873_1875delGGCinsTCAp.Gly625Ser

Exon rankN/A

missense

Prot: ENSP00000375863.2UniProt: Q9BUJ2-1

HNRNPUL1 ENST00000602130.5

TSL:1

HGVSc / HGVSpc.1873_1875delGGCinsTCAp.Gly625Ser

Exon rankN/A

missense

Prot: ENSP00000470687.1UniProt: Q9BUJ2-2

HNRNPUL1 ENST00000352456.7

TSL:1

HGVSc / HGVSpc.1573_1575delGGCinsTCAp.Gly525Ser

Exon rankN/A

missense

Prot: ENSP00000340857.3UniProt: A0A0A0MRA5

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 2 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:31
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:31

Showing 2 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Benign	3.4

Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

hg19: chr19-41808755;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar