1-4506671-T-C

Variant names:

• chr1-4506671-T-C
• rs7537577

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 0.581 in 151,992 control chromosomes in the GnomAD database, including 25,930 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 0.58 (25930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 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: 0.581 AC: 88198 AN: 151874 Hom.: 25903 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.581 AC: 88275 AN: 151992 Hom.: 25930 Cov.: 32 AF XY: 0.583 AC XY: 43311 AN XY: 74294

African (AFR) AF: 0.581 AC: 24067 AN: 41426

American (AMR) AF: 0.682 AC: 10425 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1986 AN: 3470

East Asian (EAS) AF: 0.852 AC: 4392 AN: 5152

South Asian (SAS) AF: 0.565 AC: 2721 AN: 4814

European-Finnish (FIN) AF: 0.530 AC: 5598 AN: 10558

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37018 AN: 67966

Other (OTH) AF: 0.612 AC: 1293 AN: 2114

Alfa AF: 0.551 Hom.: 4741

Bravo AF: 0.597

Asia WGS AF: 0.683 AC: 2377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.0
DANN	Benign	0.79
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs7537577; hg19: chr1-4566731; COSMIC: COSV59919787;