X-71206179-C-T

Variant names:

• chrX-71206179-C-T
• rs34640965

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 0.60 (15026 hom., 18023 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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: 0.601 AC: 64351 AN: 107162 Hom.: 15017 Cov.: 21

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.633

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: 0.601 AC: 64406 AN: 107204 Hom.: 15026 Cov.: 21 AF XY: 0.604 AC XY: 18023 AN XY: 29828

African (AFR) AF: 0.827 AC: 24497 AN: 29635

American (AMR) AF: 0.633 AC: 6233 AN: 9849

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 1770 AN: 2610

East Asian (EAS) AF: 0.753 AC: 2575 AN: 3419

South Asian (SAS) AF: 0.609 AC: 1491 AN: 2450

European-Finnish (FIN) AF: 0.399 AC: 2041 AN: 5116

Middle Eastern (MID) AF: 0.699 AC: 144 AN: 206

European-Non Finnish (NFE) AF: 0.469 AC: 24291 AN: 51819

Other (OTH) AF: 0.638 AC: 918 AN: 1438

Alfa AF: 0.543 Hom.: 4095

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.91
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs34640965; hg19: chrX-70426029;