chrX-71225931-T-C

Variant names:

• chrX-71225931-T-C
• rs1997625

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 0.52 (11192 hom., 16630 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

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: 0.521 AC: 57351 AN: 109987 Hom.: 11184 Cov.: 22

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.513

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: 0.521 AC: 57379 AN: 110041 Hom.: 11192 Cov.: 22 AF XY: 0.514 AC XY: 16630 AN XY: 32363

African (AFR) AF: 0.389 AC: 11778 AN: 30288

American (AMR) AF: 0.406 AC: 4167 AN: 10251

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1474 AN: 2625

East Asian (EAS) AF: 0.708 AC: 2456 AN: 3468

South Asian (SAS) AF: 0.476 AC: 1247 AN: 2621

European-Finnish (FIN) AF: 0.615 AC: 3540 AN: 5752

Middle Eastern (MID) AF: 0.600 AC: 129 AN: 215

European-Non Finnish (NFE) AF: 0.595 AC: 31347 AN: 52644

Other (OTH) AF: 0.521 AC: 786 AN: 1508

Alfa AF: 0.552 Hom.: 52000

Bravo AF: 0.502

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.78
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1997625; hg19: chrX-70445781;