chr1-25039556-T-A

Variant names:

• chr1-25039556-T-A
• rs395376

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.548 in 151,684 control chromosomes in the GnomAD database, including 22,829 homozygotes. 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: 𝑓 0.55 (22829 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83087 AN: 151566 Hom.: 22821 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.568

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.548 AC: 83119 AN: 151684 Hom.: 22829 Cov.: 31 AF XY: 0.549 AC XY: 40677 AN XY: 74122

African (AFR) AF: 0.490 AC: 20243 AN: 41302

American (AMR) AF: 0.571 AC: 8717 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1891 AN: 3466

East Asian (EAS) AF: 0.733 AC: 3773 AN: 5150

South Asian (SAS) AF: 0.594 AC: 2859 AN: 4816

European-Finnish (FIN) AF: 0.555 AC: 5836 AN: 10506

Middle Eastern (MID) AF: 0.586 AC: 170 AN: 290

European-Non Finnish (NFE) AF: 0.558 AC: 37861 AN: 67870

Other (OTH) AF: 0.572 AC: 1205 AN: 2106

Alfa AF: 0.542 Hom.: 2661

Bravo AF: 0.550

Asia WGS AF: 0.664 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.0
DANN	Benign	0.84
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs395376; hg19: chr1-25366047; COSMIC: COSV69619390;