rs5911500

Variant names:

• chrX-116708191-G-A
• rs5911500

Your query was ambiguous. Multiple possible variants found:

• chrX-116708191-G-A
• chrX-116708191-G-T

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 0.122 in 110,608 control chromosomes in the GnomAD database, including 737 homozygotes. There are 3,865 hemizygotes in GnomAD. 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 0.12 (737 hom., 3865 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 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: 0.122 AC: 13511 AN: 110550 Hom.: 739 Cov.: 22 AF XY: 0.118 AC XY: 3864 AN XY: 32776

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0913

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0720

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.122 AC: 13504 AN: 110608 Hom.: 737 Cov.: 22 AF XY: 0.118 AC XY: 3865 AN XY: 32844

Gnomad4 AFR AF: 0.0253

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0913

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.117

Alfa AF: 0.169 Hom.: 10606

Bravo AF: 0.115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5911500; hg19: chrX-115842159;