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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs6625163; hg19: chrX-66510984;