rs204138

Variant names:

• chrX-57038379-G-A
• rs204138

Your query was ambiguous. Multiple possible variants found:

• chrX-57038379-G-A
• chrX-57038379-G-T

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 0.545 in 110,806 control chromosomes in the GnomAD database, including 14,494 homozygotes. There are 18,252 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 0.54 (14494 hom., 18252 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 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: 0.545 AC: 60376 AN: 110753 Hom.: 14502 Cov.: 23 AF XY: 0.554 AC XY: 18247 AN XY: 32965

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.545 AC: 60356 AN: 110806 Hom.: 14494 Cov.: 23 AF XY: 0.553 AC XY: 18252 AN XY: 33028

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.486

Alfa AF: 0.193 Hom.: 2402

Bravo AF: 0.503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs204138; hg19: chrX-57064812;