chrX-117663481-A-G

Variant names:

• chrX-117663481-A-G
• rs5910185

Variant summary

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

The variant allele was found at a frequency of 0.369 in 111,225 control chromosomes in the GnomAD database, including 5,565 homozygotes. There are 11,960 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 0.37 (5565 hom., 11960 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 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: 0.369 AC: 41006 AN: 111172 Hom.: 5562 Cov.: 23

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.359

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.369 AC: 41031 AN: 111225 Hom.: 5565 Cov.: 23 AF XY: 0.357 AC XY: 11960 AN XY: 33467

African (AFR) AF: 0.351 AC: 10744 AN: 30635

American (AMR) AF: 0.276 AC: 2889 AN: 10468

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 913 AN: 2639

East Asian (EAS) AF: 0.208 AC: 733 AN: 3528

South Asian (SAS) AF: 0.374 AC: 994 AN: 2660

European-Finnish (FIN) AF: 0.383 AC: 2268 AN: 5926

Middle Eastern (MID) AF: 0.366 AC: 79 AN: 216

European-Non Finnish (NFE) AF: 0.410 AC: 21690 AN: 52962

Other (OTH) AF: 0.349 AC: 529 AN: 1514

Alfa AF: 0.390 Hom.: 3336

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs5910185; hg19: chrX-116797444;