11-13271635-T-C

Variant names:

• chr11-13271635-T-C
• rs11022738

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 0.316 in 151,968 control chromosomes in the GnomAD database, including 7,760 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 0.32 (7760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 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: 0.316 AC: 47950 AN: 151850 Hom.: 7759 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.316 AC: 47959 AN: 151968 Hom.: 7760 Cov.: 32 AF XY: 0.315 AC XY: 23394 AN XY: 74280

African (AFR) AF: 0.377 AC: 15618 AN: 41386

American (AMR) AF: 0.338 AC: 5150 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3470

East Asian (EAS) AF: 0.462 AC: 2384 AN: 5158

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4824

European-Finnish (FIN) AF: 0.264 AC: 2798 AN: 10584

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18588 AN: 67978

Other (OTH) AF: 0.286 AC: 603 AN: 2108

Alfa AF: 0.298 Hom.: 1046

Bravo AF: 0.322

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.73
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs11022738; hg19: chr11-13293182;