11-49226598-C-T

Variant names:

• chr11-49226598-C-T
• rs11040291

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 0.13 in 152,132 control chromosomes in the GnomAD database, including 1,537 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 0.13 (1537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19711 AN: 152014 Hom.: 1530 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.130 AC: 19747 AN: 152132 Hom.: 1537 Cov.: 32 AF XY: 0.131 AC XY: 9721 AN XY: 74356

African (AFR) AF: 0.206 AC: 8545 AN: 41486

American (AMR) AF: 0.115 AC: 1765 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0761 AC: 264 AN: 3468

East Asian (EAS) AF: 0.172 AC: 887 AN: 5168

South Asian (SAS) AF: 0.225 AC: 1083 AN: 4814

European-Finnish (FIN) AF: 0.0705 AC: 747 AN: 10600

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0904 AC: 6146 AN: 67990

Other (OTH) AF: 0.116 AC: 246 AN: 2116

Alfa AF: 0.0494 Hom.: 53

Bravo AF: 0.132

Asia WGS AF: 0.251 AC: 872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.30
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs11040291; hg19: chr11-49248150;