chrX-117469443-T-C

Variant names:

• chrX-117469443-T-C
• rs2040962

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 0.61 (15364 hom., 20345 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

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: 0.614 AC: 67883 AN: 110632 Hom.: 15360 Cov.: 23

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.502

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.604

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: 0.614 AC: 67935 AN: 110687 Hom.: 15364 Cov.: 23 AF XY: 0.618 AC XY: 20345 AN XY: 32937

African (AFR) AF: 0.772 AC: 23501 AN: 30448

American (AMR) AF: 0.696 AC: 7226 AN: 10387

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1454 AN: 2629

East Asian (EAS) AF: 0.960 AC: 3364 AN: 3505

South Asian (SAS) AF: 0.823 AC: 2172 AN: 2639

European-Finnish (FIN) AF: 0.518 AC: 3055 AN: 5897

Middle Eastern (MID) AF: 0.502 AC: 107 AN: 213

European-Non Finnish (NFE) AF: 0.491 AC: 25919 AN: 52786

Other (OTH) AF: 0.610 AC: 918 AN: 1504

Alfa AF: 0.543 Hom.: 57108

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs2040962; hg19: chrX-116603406;