rs2532910

Variant names:

• chrX-30357207-T-A
• rs2532910

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.87 (29545 hom., 27882 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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: 0.869 AC: 95423 AN: 109843 Hom.: 29557 Cov.: 22

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.895

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.870

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.869 AC: 95459 AN: 109893 Hom.: 29545 Cov.: 22 AF XY: 0.866 AC XY: 27882 AN XY: 32181

African (AFR) AF: 0.790 AC: 23840 AN: 30179

American (AMR) AF: 0.786 AC: 8085 AN: 10281

Ashkenazi Jewish (ASJ) AF: 0.931 AC: 2428 AN: 2607

East Asian (EAS) AF: 0.882 AC: 3090 AN: 3503

South Asian (SAS) AF: 0.847 AC: 2119 AN: 2501

European-Finnish (FIN) AF: 0.911 AC: 5250 AN: 5761

Middle Eastern (MID) AF: 0.894 AC: 193 AN: 216

European-Non Finnish (NFE) AF: 0.923 AC: 48603 AN: 52662

Other (OTH) AF: 0.863 AC: 1298 AN: 1504

Alfa AF: 0.887 Hom.: 7778

Bravo AF: 0.853

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		0.023

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: rs2532910;

hg19: chrX-30375324;