7-62969063-T-C

Variant names:

• chr7-62969063-T-C
• rs1595989

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 0.819 in 151,176 control chromosomes in the GnomAD database, including 50,999 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 0.82 (50999 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.819 AC: 123644 AN: 151058 Hom.: 50952 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.819 AC: 123747 AN: 151176 Hom.: 50999 Cov.: 31 AF XY: 0.812 AC XY: 59935 AN XY: 73848

African (AFR) AF: 0.817 AC: 33812 AN: 41372

American (AMR) AF: 0.816 AC: 12288 AN: 15064

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3006 AN: 3464

East Asian (EAS) AF: 0.508 AC: 2551 AN: 5018

South Asian (SAS) AF: 0.776 AC: 3746 AN: 4828

European-Finnish (FIN) AF: 0.771 AC: 8154 AN: 10574

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57408 AN: 67552

Other (OTH) AF: 0.826 AC: 1734 AN: 2100

Alfa AF: 0.833 Hom.: 6427

Bravo AF: 0.823

Asia WGS AF: 0.652 AC: 2265 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.36

Splicing

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

Other links and lift over

dbSNP: rs1595989; hg19: chr7-62429441;