rs12975585

Variant names:

• chr19-41264326-A-C
• rs12975585
• ENST00000352456.7:c.-6+1744A>C

Your query was ambiguous. Multiple possible variants found:

• chr19-41264326-A-C
• chr19-41264326-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000352456.7(HNRNPUL1):​c.-6+1744A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000304 in 328,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0000030 (0 hom.)
• Consequence: HNRNPUL1 ENST00000352456.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000352456.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HNRNPUL1	NM_001439172.1		c.-6+1744A>C		intron	N/A	NP_001426101.1
	HNRNPUL1	NM_144732.5		c.-6+1744A>C		intron	N/A	NP_653333.1
	HNRNPUL1	NM_001439179.1		c.-6+1744A>C		intron	N/A	NP_001426108.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HNRNPUL1	ENST00000352456.7	TSL:1	c.-6+1744A>C		intron	N/A	ENSP00000340857.3
	HNRNPUL1	ENST00000599719.5	TSL:1	c.-6+1310A>C		intron	N/A	ENSP00000470172.1
	HNRNPUL1	ENST00000595018.5	TSL:2	c.-6+1744A>C		intron	N/A	ENSP00000473132.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000304 AC: 1 AN: 328582 Hom.: 0 Cov.: 5 AF XY: 0.00000602 AC XY: 1 AN XY: 166248

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 8358

American (AMR) AF: 0.00 AC: 0 AN: 8294

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9912

East Asian (EAS) AF: 0.00 AC: 0 AN: 23434

South Asian (SAS) AF: 0.00 AC: 0 AN: 9532

European-Finnish (FIN) AF: 0.0000460 AC: 1 AN: 21718

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1462

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 226658

Other (OTH) AF: 0.00 AC: 0 AN: 19214

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		0.17
PromoterAI		0.020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12975585; hg19: chr19-41770231;