X-71231039-G-A

Variant names:

• chrX-71231039-G-A
• rs2341629

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 0.59 (14516 hom., 18754 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• 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=-0.99).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.591 AC: 64887 AN: 109744 Hom.: 14504 Cov.: 22

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.616

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: 0.592 AC: 64956 AN: 109800 Hom.: 14516 Cov.: 22 AF XY: 0.584 AC XY: 18754 AN XY: 32094

African (AFR) AF: 0.752 AC: 22714 AN: 30202

American (AMR) AF: 0.705 AC: 7211 AN: 10233

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1232 AN: 2617

East Asian (EAS) AF: 0.878 AC: 3028 AN: 3450

South Asian (SAS) AF: 0.637 AC: 1653 AN: 2594

European-Finnish (FIN) AF: 0.412 AC: 2364 AN: 5740

Middle Eastern (MID) AF: 0.592 AC: 125 AN: 211

European-Non Finnish (NFE) AF: 0.482 AC: 25363 AN: 52598

Other (OTH) AF: 0.622 AC: 925 AN: 1488

Alfa AF: 0.529 Hom.: 46009

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.27
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2341629; hg19: chrX-70450889;