rs7960147

Variant names:

• chr12-46357671-C-T
• rs7960147

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 0.704 in 152,112 control chromosomes in the GnomAD database, including 39,139 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 0.70 (39139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 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: 0.703 AC: 106905 AN: 151994 Hom.: 39085 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.704 AC: 107018 AN: 152112 Hom.: 39139 Cov.: 32 AF XY: 0.701 AC XY: 52103 AN XY: 74358

African (AFR) AF: 0.910 AC: 37764 AN: 41518

American (AMR) AF: 0.626 AC: 9559 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2462 AN: 3472

East Asian (EAS) AF: 0.816 AC: 4220 AN: 5174

South Asian (SAS) AF: 0.662 AC: 3195 AN: 4824

European-Finnish (FIN) AF: 0.614 AC: 6471 AN: 10544

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41074 AN: 67988

Other (OTH) AF: 0.695 AC: 1470 AN: 2114

Alfa AF: 0.642 Hom.: 120807

Bravo AF: 0.719

Asia WGS AF: 0.751 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.48
DANN	Benign	0.31
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7960147; hg19: chr12-46751454;