rs6712766

Variant names:

• chr2-117854213-G-A
• rs6712766

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 0.139 in 152,244 control chromosomes in the GnomAD database, including 2,066 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 0.14 (2066 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 6 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 (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: 0.139 AC: 21116 AN: 152128 Hom.: 2055 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.0489

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0730

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.139 AC: 21177 AN: 152244 Hom.: 2066 Cov.: 31 AF XY: 0.142 AC XY: 10539 AN XY: 74438

African (AFR) AF: 0.271 AC: 11264 AN: 41522

American (AMR) AF: 0.136 AC: 2080 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3472

East Asian (EAS) AF: 0.0487 AC: 252 AN: 5176

South Asian (SAS) AF: 0.0659 AC: 318 AN: 4826

European-Finnish (FIN) AF: 0.163 AC: 1732 AN: 10616

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0730 AC: 4967 AN: 68016

Other (OTH) AF: 0.113 AC: 239 AN: 2114

Alfa AF: 0.0894 Hom.: 1452

Bravo AF: 0.143

Asia WGS AF: 0.0870 AC: 305 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	5.0
DANN	Benign	0.61
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs6712766; hg19: chr2-118611789; COSMIC: COSV60099933;