X-136262171-T-C

Variant names:

• chrX-136262171-T-C
• rs5975710

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 (10716 hom., 17219 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• 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=-0.93).

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: 0.520 AC: 57632 AN: 110906 Hom.: 10716 Cov.: 23

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.393

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.468

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: 0.520 AC: 57655 AN: 110961 Hom.: 10716 Cov.: 23 AF XY: 0.518 AC XY: 17219 AN XY: 33225

African (AFR) AF: 0.440 AC: 13449 AN: 30551

American (AMR) AF: 0.496 AC: 5189 AN: 10469

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1304 AN: 2638

East Asian (EAS) AF: 0.709 AC: 2478 AN: 3496

South Asian (SAS) AF: 0.487 AC: 1282 AN: 2635

European-Finnish (FIN) AF: 0.611 AC: 3606 AN: 5899

Middle Eastern (MID) AF: 0.373 AC: 79 AN: 212

European-Non Finnish (NFE) AF: 0.552 AC: 29210 AN: 52870

Other (OTH) AF: 0.470 AC: 712 AN: 1514

Alfa AF: 0.563 Hom.: 4172

Bravo AF: 0.513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.25
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs5975710; hg19: chrX-135344330;