chrX-130270608-C-T

Variant names:

• chrX-130270608-C-T
• rs5975178

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 0.541 in 110,691 control chromosomes in the GnomAD database, including 12,809 homozygotes. There are 17,659 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 (12809 hom., 17659 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.541 AC: 59860 AN: 110637 Hom.: 12809 Cov.: 23

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.541 AC: 59921 AN: 110691 Hom.: 12809 Cov.: 23 AF XY: 0.536 AC XY: 17659 AN XY: 32919

African (AFR) AF: 0.817 AC: 24893 AN: 30467

American (AMR) AF: 0.491 AC: 5093 AN: 10383

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1403 AN: 2623

East Asian (EAS) AF: 0.359 AC: 1264 AN: 3519

South Asian (SAS) AF: 0.560 AC: 1486 AN: 2652

European-Finnish (FIN) AF: 0.433 AC: 2505 AN: 5782

Middle Eastern (MID) AF: 0.583 AC: 126 AN: 216

European-Non Finnish (NFE) AF: 0.414 AC: 21863 AN: 52868

Other (OTH) AF: 0.541 AC: 817 AN: 1510

Alfa AF: 0.490 Hom.: 3583

Bravo AF: 0.558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.49
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs5975178; hg19: chrX-129404582;