11-124858227-T-G

Variant names:

• chr11-124858227-T-G
• rs11219814

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 0.18 in 151,528 control chromosomes in the GnomAD database, including 2,844 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 0.18 (2844 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.699
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 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: 0.181 AC: 27334 AN: 151410 Hom.: 2843 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.00348

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.180 AC: 27345 AN: 151528 Hom.: 2844 Cov.: 31 AF XY: 0.182 AC XY: 13460 AN XY: 74014

African (AFR) AF: 0.106 AC: 4374 AN: 41350

American (AMR) AF: 0.157 AC: 2398 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3462

East Asian (EAS) AF: 0.00349 AC: 18 AN: 5158

South Asian (SAS) AF: 0.157 AC: 753 AN: 4810

European-Finnish (FIN) AF: 0.288 AC: 2979 AN: 10346

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.227 AC: 15397 AN: 67860

Other (OTH) AF: 0.193 AC: 407 AN: 2112

Alfa AF: 0.202 Hom.: 4359

Bravo AF: 0.165

Asia WGS AF: 0.0690 AC: 244 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.65
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs11219814; hg19: chr11-124728123; COSMIC: COSV53397824;