rs6712932

chr2-105221141-T-C

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/exons	MANE	UniProt

Ensembl

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