X-151925526-G-A

Variant names:

• chrX-151925526-G-A
• rs5970160

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 0.221 in 111,003 control chromosomes in the GnomAD database, including 3,237 homozygotes. There are 6,994 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 0.22 (3237 hom., 6994 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.221 AC: 24539 AN: 110949 Hom.: 3240 Cov.: 22

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.0611

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00926

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.221 AC: 24576 AN: 111003 Hom.: 3237 Cov.: 22 AF XY: 0.210 AC XY: 6994 AN XY: 33245

African (AFR) AF: 0.503 AC: 15249 AN: 30332

American (AMR) AF: 0.119 AC: 1249 AN: 10518

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 300 AN: 2623

East Asian (EAS) AF: 0.00902 AC: 32 AN: 3549

South Asian (SAS) AF: 0.195 AC: 511 AN: 2622

European-Finnish (FIN) AF: 0.172 AC: 1020 AN: 5942

Middle Eastern (MID) AF: 0.117 AC: 25 AN: 213

European-Non Finnish (NFE) AF: 0.110 AC: 5836 AN: 53008

Other (OTH) AF: 0.207 AC: 312 AN: 1509

Alfa AF: 0.154 Hom.: 11699

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs5970160; hg19: chrX-151093998;