X-67291142-G-A

Variant names:

• chrX-67291142-G-A
• rs6625163

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 0.64 (19206 hom., 20534 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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: 0.637 AC: 69381 AN: 108944 Hom.: 19215 Cov.: 22

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.682

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: 0.636 AC: 69361 AN: 108980 Hom.: 19206 Cov.: 22 AF XY: 0.654 AC XY: 20534 AN XY: 31420

African (AFR) AF: 0.136 AC: 4071 AN: 30000

American (AMR) AF: 0.821 AC: 8389 AN: 10222

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 2350 AN: 2622

East Asian (EAS) AF: 0.998 AC: 3422 AN: 3428

South Asian (SAS) AF: 0.914 AC: 2284 AN: 2500

European-Finnish (FIN) AF: 0.813 AC: 4367 AN: 5374

Middle Eastern (MID) AF: 0.758 AC: 157 AN: 207

European-Non Finnish (NFE) AF: 0.814 AC: 42717 AN: 52476

Other (OTH) AF: 0.685 AC: 1011 AN: 1475

Alfa AF: 0.771 Hom.: 119799

Bravo AF: 0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		0.13

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: rs6625163;

hg19: chrX-66510984;