rs178995

Variant names:

• chrX-12902467-A-G
• rs178995

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 0.188 in 110,894 control chromosomes in the GnomAD database, including 1,643 homozygotes. There are 5,901 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 0.19 (1643 hom., 5901 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 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: 0.188 AC: 20798 AN: 110840 Hom.: 1644 Cov.: 22

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.00643

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.188 AC: 20808 AN: 110894 Hom.: 1643 Cov.: 22 AF XY: 0.178 AC XY: 5901 AN XY: 33184

African (AFR) AF: 0.285 AC: 8649 AN: 30351

American (AMR) AF: 0.127 AC: 1329 AN: 10449

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 310 AN: 2634

East Asian (EAS) AF: 0.00645 AC: 23 AN: 3567

South Asian (SAS) AF: 0.0891 AC: 238 AN: 2672

European-Finnish (FIN) AF: 0.198 AC: 1163 AN: 5882

Middle Eastern (MID) AF: 0.123 AC: 26 AN: 212

European-Non Finnish (NFE) AF: 0.165 AC: 8739 AN: 52946

Other (OTH) AF: 0.163 AC: 246 AN: 1507

Alfa AF: 0.194 Hom.: 1109

Bravo AF: 0.191

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs178995; hg19: chrX-12920586;