X-43749435-A-T

Variant names:

• chrX-43749435-A-T
• rs2064070

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 (16665 hom., 20438 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 15 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).

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: 0.643 AC: 71076 AN: 110587 Hom.: 16668 Cov.: 23

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.651

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: 0.643 AC: 71105 AN: 110640 Hom.: 16665 Cov.: 23 AF XY: 0.622 AC XY: 20438 AN XY: 32880

African (AFR) AF: 0.622 AC: 18893 AN: 30394

American (AMR) AF: 0.627 AC: 6551 AN: 10452

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 1867 AN: 2632

East Asian (EAS) AF: 0.423 AC: 1473 AN: 3486

South Asian (SAS) AF: 0.373 AC: 974 AN: 2612

European-Finnish (FIN) AF: 0.556 AC: 3268 AN: 5877

Middle Eastern (MID) AF: 0.738 AC: 158 AN: 214

European-Non Finnish (NFE) AF: 0.693 AC: 36560 AN: 52782

Other (OTH) AF: 0.648 AC: 980 AN: 1513

Alfa AF: 0.667 Hom.: 5228

Bravo AF: 0.647

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.36
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs2064070; hg19: chrX-43608682;