rs6712932

Variant names:

• chr2-105221141-T-C
• rs6712932

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 0.311 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.342

Alfa AF: 0.333 Hom.: 20286

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

Splicing

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

Publications

LitVar

Other links and lift over

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