Variant 5-179616220-TGTTAA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_001257293.2(HNRNPH1):c.1208-7_1208-3del variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.00195 in 1,613,524 control chromosomes in the GnomAD database, including 14 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0053 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0016 ( 6 hom. )

Consequence

HNRNPH1
NM_001257293.2 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.97

Variant links:

Genes affected

HNRNPH1 (HGNC:5041): (heterogeneous nuclear ribonucleoprotein H1) This gene encodes a member of a subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins that complex with heterogeneous nuclear RNA. These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some may shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has three repeats of quasi-RRM domains that bind to RNA and is very similar to the family member HNRPF. This gene may be associated with hereditary lymphedema type I. Alternatively spliced transcript variants have been described [provided by RefSeq, Mar 2012]

HNRNPH1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-179616220-TGTTAA-T is Benign according to our data. Variant chr5-179616220-TGTTAA-T is described in ClinVar as [Benign]. Clinvar id is 768054.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00532 (810/152346) while in subpopulation AFR AF= 0.0164 (682/41588). AF 95% confidence interval is 0.0154. There are 8 homozygotes in gnomad4. There are 376 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 810 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HNRNPH1	NM_001257293.2 linkuse as main transcript	c.1208-7_1208-3del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000393432.9	NP_001244222.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNRNPH1	ENST00000393432.9 linkuse as main transcript	c.1208-7_1208-3del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_001257293.2	ENSP00000377082	P4

Frequencies

GnomAD3 genomes

AF:

0.00532

AC:

810

AN:

152228

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0164

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00144

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00109

Gnomad OTH

AF:

0.00622

GnomAD3 exomes

AF:

0.00230

AC:

579

AN:

251468

Hom.:

AF XY:

0.00195

AC XY:

265

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.0175

Gnomad AMR exome

AF:

0.00145

Gnomad ASJ exome

AF:

0.000992

Gnomad EAS exome

AF:

0.00147

Gnomad SAS exome

AF:

0.00167

Gnomad FIN exome

AF:

0.000277

Gnomad NFE exome

AF:

0.00125

Gnomad OTH exome

AF:

0.00147

GnomAD4 exome

AF:

0.00160

AC:

2337

AN:

1461178

Hom.:

AF XY:

0.00158

AC XY:

1146

AN XY:

726972

show subpopulations

Gnomad4 AFR exome

AF:

0.0186

Gnomad4 AMR exome

AF:

0.00159

Gnomad4 ASJ exome

AF:

0.000574

Gnomad4 EAS exome

AF:

0.00103

Gnomad4 SAS exome

AF:

0.00141

Gnomad4 FIN exome

AF:

0.000225

Gnomad4 NFE exome

AF:

0.00117

Gnomad4 OTH exome

AF:

0.00235

GnomAD4 genome

AF:

0.00532

AC:

810

AN:

152346

Hom.:

Cov.:

AF XY:

0.00505

AC XY:

376

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.0164

Gnomad4 AMR

AF:

0.00144

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00154

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00109

Gnomad4 OTH

AF:

0.00616

Alfa

AF:

0.00305

Hom.:

Bravo

AF:

0.00593

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.00142

EpiControl

AF:

0.00124

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 14, 2018

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over