11-1262997-A-G

Variant names:

• chr11-1262997-A-G
• rs12417955

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 0.535 in 517,910 control chromosomes in the GnomAD database, including 74,904 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 0.54 (22376 hom., cov: 33)
  • Exomes 𝑓: 0.53 (52528 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82030 AN: 151880 Hom.: 22342 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.545

GnomAD2 exomes AF: 0.549 AC: 125515 AN: 228708 AF XY: 0.541

Gnomad AFR exome AF: 0.559

Gnomad AMR exome AF: 0.622

Gnomad ASJ exome AF: 0.544

Gnomad EAS exome AF: 0.671

Gnomad FIN exome AF: 0.576

Gnomad NFE exome AF: 0.509

Gnomad OTH exome AF: 0.542

GnomAD4 exome AF: 0.533 AC: 194950 AN: 365912 Hom.: 52528 Cov.: 0 AF XY: 0.526 AC XY: 109335 AN XY: 207946

African (AFR) AF: 0.559 AC: 5683 AN: 10158

American (AMR) AF: 0.622 AC: 21921 AN: 35230

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 5873 AN: 10898

East Asian (EAS) AF: 0.673 AC: 8421 AN: 12520

South Asian (SAS) AF: 0.508 AC: 33156 AN: 65266

European-Finnish (FIN) AF: 0.575 AC: 17423 AN: 30320

Middle Eastern (MID) AF: 0.517 AC: 1406 AN: 2720

European-Non Finnish (NFE) AF: 0.507 AC: 92599 AN: 182768

Other (OTH) AF: 0.528 AC: 8468 AN: 16032

GnomAD4 genome AF: 0.540 AC: 82116 AN: 151998 Hom.: 22376 Cov.: 33 AF XY: 0.546 AC XY: 40529 AN XY: 74290

African (AFR) AF: 0.559 AC: 23148 AN: 41446

American (AMR) AF: 0.592 AC: 9049 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1878 AN: 3464

East Asian (EAS) AF: 0.667 AC: 3434 AN: 5148

South Asian (SAS) AF: 0.512 AC: 2470 AN: 4822

European-Finnish (FIN) AF: 0.587 AC: 6211 AN: 10586

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34117 AN: 67932

Other (OTH) AF: 0.548 AC: 1154 AN: 2106

Alfa AF: 0.513 Hom.: 11423

Bravo AF: 0.543

Asia WGS AF: 0.622 AC: 2165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs12417955; hg19: chr11-1284227; COSMIC: COSV101500483;