X-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).

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: 0.580 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 v4.3

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;