rs5911500

Variant names:

• chrX-116708191-G-A
• rs5911500
• ENST00000842004.1:n.390-14958C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000842004.1(ENSG00000230159):​n.390-14958C>T variant causes a intron change. 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: ENSG00000230159 ENST00000842004.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 4 publications found

Genes affected

ENSG00000230159 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842004.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230159	ENST00000842004.1		n.390-14958C>T		intron	N/A
	ENSG00000230159	ENST00000842005.1		n.338-14958C>T		intron	N/A
	ENSG00000230159	ENST00000842006.1		n.145-14958C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 13511 AN: 110550 Hom.: 739 Cov.: 22

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

African (AFR) AF: 0.0253 AC: 772 AN: 30508

American (AMR) AF: 0.101 AC: 1050 AN: 10418

Ashkenazi Jewish (ASJ) AF: 0.0913 AC: 240 AN: 2629

East Asian (EAS) AF: 0.121 AC: 420 AN: 3472

South Asian (SAS) AF: 0.116 AC: 300 AN: 2596

European-Finnish (FIN) AF: 0.159 AC: 934 AN: 5868

Middle Eastern (MID) AF: 0.0837 AC: 18 AN: 215

European-Non Finnish (NFE) AF: 0.180 AC: 9485 AN: 52721

Other (OTH) AF: 0.117 AC: 177 AN: 1509

Alfa AF: 0.153 Hom.: 13434

Bravo AF: 0.115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5911500;

hg19: chrX-115842159;