X-42831917-C-T

Variant names:

• chrX-42831917-C-T
• rs5991601

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 0.0861 in 111,353 control chromosomes in the GnomAD database, including 399 homozygotes. There are 2,761 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 0.086 (399 hom., 2761 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 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: 0.0861 AC: 9586 AN: 111298 Hom.: 398 Cov.: 22

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00146

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.0932

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.0861 AC: 9586 AN: 111353 Hom.: 399 Cov.: 22 AF XY: 0.0822 AC XY: 2761 AN XY: 33587

African (AFR) AF: 0.125 AC: 3836 AN: 30628

American (AMR) AF: 0.0600 AC: 631 AN: 10517

Ashkenazi Jewish (ASJ) AF: 0.0580 AC: 153 AN: 2637

East Asian (EAS) AF: 0.266 AC: 926 AN: 3477

South Asian (SAS) AF: 0.143 AC: 381 AN: 2660

European-Finnish (FIN) AF: 0.0541 AC: 324 AN: 5992

Middle Eastern (MID) AF: 0.0884 AC: 19 AN: 215

European-Non Finnish (NFE) AF: 0.0599 AC: 3177 AN: 53029

Other (OTH) AF: 0.0911 AC: 138 AN: 1514

Alfa AF: 0.0700 Hom.: 441

Bravo AF: 0.0916

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.30
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs5991601; hg19: chrX-42691167;