rs6711016

Variant names:

• chr2-20923592-C-A
• rs6711016

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 0.2 in 152,140 control chromosomes in the GnomAD database, including 3,972 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 0.20 (3972 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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: 0.200 AC: 30463 AN: 152022 Hom.: 3975 Cov.: 33

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.200 AC: 30453 AN: 152140 Hom.: 3972 Cov.: 33 AF XY: 0.206 AC XY: 15324 AN XY: 74372

African (AFR) AF: 0.0578 AC: 2402 AN: 41536

American (AMR) AF: 0.224 AC: 3418 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2836 AN: 5164

South Asian (SAS) AF: 0.366 AC: 1760 AN: 4814

European-Finnish (FIN) AF: 0.276 AC: 2921 AN: 10588

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15777 AN: 67966

Other (OTH) AF: 0.224 AC: 475 AN: 2116

Alfa AF: 0.225 Hom.: 13544

Bravo AF: 0.189

Asia WGS AF: 0.445 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.53
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6711016; hg19: chr2-21123352;