X-117705471-T-C

Variant names:

• chrX-117705471-T-C
• rs4825536

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 0.394 in 110,000 control chromosomes in the GnomAD database, including 6,518 homozygotes. There are 12,641 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 0.39 (6518 hom., 12641 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 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: 0.394 AC: 43349 AN: 109948 Hom.: 6519 Cov.: 22

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.390

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.394 AC: 43386 AN: 110000 Hom.: 6518 Cov.: 22 AF XY: 0.391 AC XY: 12641 AN XY: 32366

African (AFR) AF: 0.527 AC: 15946 AN: 30271

American (AMR) AF: 0.331 AC: 3434 AN: 10377

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 942 AN: 2624

East Asian (EAS) AF: 0.520 AC: 1798 AN: 3457

South Asian (SAS) AF: 0.457 AC: 1183 AN: 2590

European-Finnish (FIN) AF: 0.338 AC: 1954 AN: 5788

Middle Eastern (MID) AF: 0.389 AC: 82 AN: 211

European-Non Finnish (NFE) AF: 0.330 AC: 17344 AN: 52508

Other (OTH) AF: 0.390 AC: 584 AN: 1497

Alfa AF: 0.355 Hom.: 2241

Bravo AF: 0.401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.41
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs4825536; hg19: chrX-116839434;