rs7976504

Variant names:

• chr12-131386529-G-A
• rs7976504

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 0.134 in 152,112 control chromosomes in the GnomAD database, including 1,947 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 0.13 (1947 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.23).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 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: 0.134 AC: 20358 AN: 151994 Hom.: 1944 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0797

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.0986

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.134 AC: 20381 AN: 152112 Hom.: 1947 Cov.: 33 AF XY: 0.131 AC XY: 9716 AN XY: 74370

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.0740

Gnomad4 ASJ AF: 0.0797

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.0986

Gnomad4 NFE AF: 0.0893

Gnomad4 OTH AF: 0.114

Alfa AF: 0.105 Hom.: 206

Bravo AF: 0.138

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.50
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7976504; hg19: chr12-131871074;