rs4271113

Variant names:

• chrX-34874386-G-A
• rs4271113

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 0.143 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.121 AC: 3682 AN: 30479

American (AMR) AF: 0.236 AC: 2393 AN: 10158

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 441 AN: 2638

East Asian (EAS) AF: 0.480 AC: 1631 AN: 3398

South Asian (SAS) AF: 0.278 AC: 729 AN: 2624

European-Finnish (FIN) AF: 0.114 AC: 647 AN: 5670

Middle Eastern (MID) AF: 0.100 AC: 21 AN: 209

European-Non Finnish (NFE) AF: 0.110 AC: 5802 AN: 52942

Other (OTH) AF: 0.159 AC: 236 AN: 1481

Alfa AF: 0.134 Hom.: 10221

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4271113; hg19: chrX-34892503;