rs925178

Variant names:

• chrX-42988913-C-T
• rs925178

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 0.411 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.411 AC: 45393 AN: 110438 Hom.: 6905 Cov.: 22

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

African (AFR) AF: 0.307 AC: 9369 AN: 30494

American (AMR) AF: 0.561 AC: 5787 AN: 10315

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1029 AN: 2634

East Asian (EAS) AF: 0.713 AC: 2459 AN: 3449

South Asian (SAS) AF: 0.489 AC: 1281 AN: 2622

European-Finnish (FIN) AF: 0.522 AC: 3049 AN: 5839

Middle Eastern (MID) AF: 0.409 AC: 88 AN: 215

European-Non Finnish (NFE) AF: 0.409 AC: 21561 AN: 52754

Other (OTH) AF: 0.425 AC: 636 AN: 1498

Alfa AF: 0.413 Hom.: 43260

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs925178; hg19: chrX-42848162;