rs6712932

Variant names:

• chr2-105221141-T-C
• rs6712932

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 0.311 in 152,054 control chromosomes in the GnomAD database, including 7,488 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 0.31 (7488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.331 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: 0.311 AC: 47225 AN: 151936 Hom.: 7488 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.311 AC: 47237 AN: 152054 Hom.: 7488 Cov.: 32 AF XY: 0.309 AC XY: 22978 AN XY: 74316

African (AFR) AF: 0.268 AC: 11089 AN: 41444

American (AMR) AF: 0.338 AC: 5174 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1673 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1197 AN: 5176

South Asian (SAS) AF: 0.300 AC: 1445 AN: 4816

European-Finnish (FIN) AF: 0.289 AC: 3054 AN: 10556

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22398 AN: 67988

Other (OTH) AF: 0.342 AC: 720 AN: 2108

Alfa AF: 0.327 Hom.: 39071

Bravo AF: 0.314

Asia WGS AF: 0.245 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.89
DANN	Benign	0.69
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6712932; hg19: chr2-105837598; COSMIC: COSV60087685;