rs916457

Variant names:

• chr11-637014-C-T
• rs916457

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 0.0766 in 152,138 control chromosomes in the GnomAD database, including 544 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 0.077 (544 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0765 AC: 11633 AN: 152026 Hom.: 541 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0529

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0766 AC: 11659 AN: 152138 Hom.: 544 Cov.: 32 AF XY: 0.0777 AC XY: 5783 AN XY: 74380

African (AFR) AF: 0.102 AC: 4229 AN: 41534

American (AMR) AF: 0.131 AC: 2007 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 187 AN: 3468

East Asian (EAS) AF: 0.134 AC: 689 AN: 5138

South Asian (SAS) AF: 0.105 AC: 506 AN: 4818

European-Finnish (FIN) AF: 0.0238 AC: 253 AN: 10618

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0529 AC: 3594 AN: 67970

Other (OTH) AF: 0.0671 AC: 142 AN: 2116

Alfa AF: 0.0800 Hom.: 123

Bravo AF: 0.0806

Asia WGS AF: 0.136 AC: 470 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.93
PhyloP100		1.1
PromoterAI		0.0011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs916457; hg19: chr11-637014;