rs1263177

Variant names:

• chr11-116819996-C-T
• rs1263177

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 0.615 in 151,856 control chromosomes in the GnomAD database, including 28,721 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 0.61 (28721 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 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: 0.615 AC: 93297 AN: 151738 Hom.: 28722 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.615 AC: 93326 AN: 151856 Hom.: 28721 Cov.: 31 AF XY: 0.607 AC XY: 45068 AN XY: 74246

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.615

Alfa AF: 0.617 Hom.: 3603

Bravo AF: 0.626

Asia WGS AF: 0.552 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.26
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1263177; hg19: chr11-116690712;