chrX-44795709-C-T

Variant names:

• chrX-44795709-C-T
• rs548996

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 0.58 (13525 hom., 18531 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.09
• 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=-1.04).

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: 0.580 AC: 63516 AN: 109589 Hom.: 13518 Cov.: 22

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.573

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: 0.580 AC: 63551 AN: 109645 Hom.: 13525 Cov.: 22 AF XY: 0.580 AC XY: 18531 AN XY: 31953

African (AFR) AF: 0.457 AC: 13785 AN: 30166

American (AMR) AF: 0.649 AC: 6535 AN: 10077

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1407 AN: 2634

East Asian (EAS) AF: 0.262 AC: 908 AN: 3464

South Asian (SAS) AF: 0.467 AC: 1213 AN: 2600

European-Finnish (FIN) AF: 0.645 AC: 3643 AN: 5647

Middle Eastern (MID) AF: 0.481 AC: 100 AN: 208

European-Non Finnish (NFE) AF: 0.655 AC: 34505 AN: 52674

Other (OTH) AF: 0.569 AC: 855 AN: 1503

Alfa AF: 0.629 Hom.: 86139

Bravo AF: 0.580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.70
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs548996; hg19: chrX-44654955;