rs1263167

Positions:

• chr11-116807007-A-G

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 0.134 in 152,238 control chromosomes in the GnomAD database, including 1,817 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 (1817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20441 AN: 152120 Hom.: 1819 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.134 AC: 20450 AN: 152238 Hom.: 1817 Cov.: 32 AF XY: 0.131 AC XY: 9730 AN XY: 74438

Gnomad4 AFR AF: 0.0389

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.146

Alfa AF: 0.180 Hom.: 1419

Bravo AF: 0.127

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.79
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1263167; hg19: chr11-116677723;