11-4274989-G-C

Variant names:

• chr11-4274989-G-C
• rs11031481

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 0.108 in 147,510 control chromosomes in the GnomAD database, including 2,208 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 0.11 (2208 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 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: 0.108 AC: 15913 AN: 147412 Hom.: 2210 Cov.: 29

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.108 AC: 15900 AN: 147510 Hom.: 2208 Cov.: 29 AF XY: 0.106 AC XY: 7646 AN XY: 71888

African (AFR) AF: 0.0311 AC: 1255 AN: 40290

American (AMR) AF: 0.109 AC: 1580 AN: 14518

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 425 AN: 3366

East Asian (EAS) AF: 0.194 AC: 921 AN: 4746

South Asian (SAS) AF: 0.196 AC: 883 AN: 4508

European-Finnish (FIN) AF: 0.116 AC: 1198 AN: 10368

Middle Eastern (MID) AF: 0.140 AC: 40 AN: 286

European-Non Finnish (NFE) AF: 0.139 AC: 9260 AN: 66536

Other (OTH) AF: 0.102 AC: 208 AN: 2038

Alfa AF: 0.0374 Hom.: 70

Asia WGS AF: 0.193 AC: 638 AN: 3316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.19
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs11031481; hg19: chr11-4296219;