rs4271113

Variant names:

• chrX-34874386-G-A
• rs4271113

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;