11-13275014-T-C

Variant names:

• chr11-13275014-T-C
• rs11022742

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 0.25 in 152,020 control chromosomes in the GnomAD database, including 5,109 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 0.25 (5109 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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: 0.250 AC: 38013 AN: 151902 Hom.: 5111 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.250 AC: 38005 AN: 152020 Hom.: 5109 Cov.: 31 AF XY: 0.252 AC XY: 18706 AN XY: 74312

African (AFR) AF: 0.148 AC: 6141 AN: 41464

American (AMR) AF: 0.316 AC: 4836 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3466

East Asian (EAS) AF: 0.464 AC: 2398 AN: 5166

South Asian (SAS) AF: 0.304 AC: 1465 AN: 4812

European-Finnish (FIN) AF: 0.265 AC: 2793 AN: 10556

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18545 AN: 67962

Other (OTH) AF: 0.233 AC: 490 AN: 2106

Alfa AF: 0.257 Hom.: 5739

Bravo AF: 0.246

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.7
DANN	Benign	0.67
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs11022742; hg19: chr11-13296561;