rs242908

Variant names:

• chrX-132605666-G-A
• rs242908

Your query was ambiguous. Multiple possible variants found:

• chrX-132605666-G-A
• chrX-132605666-G-T

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 0.543 in 110,577 control chromosomes in the GnomAD database, including 13,732 homozygotes. There are 17,292 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 (13732 hom., 17292 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 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: 0.543 AC: 60019 AN: 110519 Hom.: 13724 Cov.: 22

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.543 AC: 60072 AN: 110577 Hom.: 13732 Cov.: 22 AF XY: 0.527 AC XY: 17292 AN XY: 32817

African (AFR) AF: 0.894 AC: 27153 AN: 30373

American (AMR) AF: 0.371 AC: 3867 AN: 10411

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 934 AN: 2636

East Asian (EAS) AF: 0.463 AC: 1602 AN: 3458

South Asian (SAS) AF: 0.457 AC: 1188 AN: 2599

European-Finnish (FIN) AF: 0.375 AC: 2197 AN: 5859

Middle Eastern (MID) AF: 0.519 AC: 111 AN: 214

European-Non Finnish (NFE) AF: 0.419 AC: 22119 AN: 52826

Other (OTH) AF: 0.528 AC: 803 AN: 1521

Alfa AF: 0.468 Hom.: 51190

Bravo AF: 0.554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs242908;

hg19: chrX-131739694;