rs204141

Variant names:

• chrX-57041275-G-A
• rs204141

Your query was ambiguous. Multiple possible variants found:

• chrX-57041275-G-A
• chrX-57041275-G-C
• chrX-57041275-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 110,297 control chromosomes in the GnomAD database, including 14,490 homozygotes. There are 18,022 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 (14490 hom., 18022 hem., cov: 22)
• 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=-0.67).
• 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: 60132 AN: 110240 Hom.: 14498 Cov.: 22 AF XY: 0.554 AC XY: 18018 AN XY: 32504

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.371

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.545 AC: 60111 AN: 110297 Hom.: 14490 Cov.: 22 AF XY: 0.553 AC XY: 18022 AN XY: 32571

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.490

Alfa AF: 0.482 Hom.: 2401

Bravo AF: 0.503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.7
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs204141; hg19: chrX-57067708;