rs7976059

Variant names:

• chr12-51857488-G-T
• rs7976059

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 0.357 in 151,832 control chromosomes in the GnomAD database, including 10,071 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 0.36 (10071 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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: 0.357 AC: 54130 AN: 151714 Hom.: 10054 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.357 AC: 54182 AN: 151832 Hom.: 10071 Cov.: 31 AF XY: 0.361 AC XY: 26812 AN XY: 74214

African (AFR) AF: 0.295 AC: 12196 AN: 41408

American (AMR) AF: 0.429 AC: 6546 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3472

East Asian (EAS) AF: 0.688 AC: 3517 AN: 5112

South Asian (SAS) AF: 0.400 AC: 1922 AN: 4804

European-Finnish (FIN) AF: 0.376 AC: 3961 AN: 10522

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23591 AN: 67928

Other (OTH) AF: 0.344 AC: 726 AN: 2108

Alfa AF: 0.356 Hom.: 44460

Bravo AF: 0.359

Asia WGS AF: 0.524 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.55
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs7976059; hg19: chr12-52251272;