rs7960147

Variant names:

• chr12-46357671-C-T
• rs7960147

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.703 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

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.695

Alfa AF: 0.629 Hom.: 51737

Bravo AF: 0.719

Asia WGS AF: 0.751 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7960147; hg19: chr12-46751454;