chrX-117705471-T-C

Variant names:

• chrX-117705471-T-C
• rs4825536

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 0.394 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

ACMG classification

Verdict is Benign. Variant got -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 AF XY: 0.390 AC XY: 12609 AN XY: 32304

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

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.390

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4825536; hg19: chrX-116839434;