X-57041275-G-A

Position:

• chrX-57041275-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 0.545 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;