rs925178

Positions:

• chrX-42988913-C-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 0.411 in 110,494 control chromosomes in the GnomAD database, including 6,911 homozygotes. There are 13,619 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 0.41 (6911 hom., 13619 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.411 AC: 45393 AN: 110438 Hom.: 6905 Cov.: 22 AF XY: 0.416 AC XY: 13597 AN XY: 32724

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.411 AC: 45415 AN: 110494 Hom.: 6911 Cov.: 22 AF XY: 0.415 AC XY: 13619 AN XY: 32790

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.425

Alfa AF: 0.416 Hom.: 31786

Bravo AF: 0.421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
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: rs925178; hg19: chrX-42848162;