chrX-34874386-G-A

Position:

• chrX-34874386-G-A

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 0.143 in 110,272 control chromosomes in the GnomAD database, including 1,050 homozygotes. There are 4,588 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 0.14 (1050 hom., 4588 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.143 AC: 15761 AN: 110213 Hom.: 1051 Cov.: 22 AF XY: 0.141 AC XY: 4580 AN XY: 32501

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.143 AC: 15768 AN: 110272 Hom.: 1050 Cov.: 22 AF XY: 0.141 AC XY: 4588 AN XY: 32566

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.159

Alfa AF: 0.129 Hom.: 6585

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4271113; hg19: chrX-34892503;