rs7960147

chr12-46357671-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;