rs7963521

Variant names:

• chr12-73435176-C-T
• rs7963521

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 0.595 in 151,994 control chromosomes in the GnomAD database, including 26,997 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 0.59 (26997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 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: 0.595 AC: 90314 AN: 151876 Hom.: 26984 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.595 AC: 90365 AN: 151994 Hom.: 26997 Cov.: 32 AF XY: 0.593 AC XY: 44077 AN XY: 74302

African (AFR) AF: 0.597 AC: 24737 AN: 41458

American (AMR) AF: 0.569 AC: 8698 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1931 AN: 3472

East Asian (EAS) AF: 0.769 AC: 3960 AN: 5150

South Asian (SAS) AF: 0.611 AC: 2945 AN: 4822

European-Finnish (FIN) AF: 0.532 AC: 5613 AN: 10552

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40463 AN: 67950

Other (OTH) AF: 0.622 AC: 1313 AN: 2110

Alfa AF: 0.594 Hom.: 53741

Bravo AF: 0.596

Asia WGS AF: 0.680 AC: 2361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7963521; hg19: chr12-73828956;