chrX-43749435-A-T

Position:

• chrX-43749435-A-T

Variant summary

Our verdict is Likely benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.43749435A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.643 AC: 71076 AN: 110587 Hom.: 16668 Cov.: 23 AF XY: 0.622 AC XY: 20400 AN XY: 32817

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

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.648

Alfa AF: 0.667 Hom.: 5228

Bravo AF: 0.647

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2064070; hg19: chrX-43608682;