chr11-637014-C-T

Variant names:

• chr11-637014-C-T
• rs916457

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0765 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

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0529

Gnomad4 OTH AF: 0.0671

Alfa AF: 0.0614 Hom.: 41

Bravo AF: 0.0806

Asia WGS AF: 0.136 AC: 470 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916457; hg19: chr11-637014;