rs239748

Variant names:

• chrX-18865240-T-C
• rs239748

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 0.65 (18619 hom., 20392 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• 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=-0.75).

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: 0.646 AC: 70679 AN: 109374 Hom.: 18628 Cov.: 22

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.656

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: 0.646 AC: 70668 AN: 109431 Hom.: 18619 Cov.: 22 AF XY: 0.643 AC XY: 20392 AN XY: 31731

African (AFR) AF: 0.265 AC: 7990 AN: 30179

American (AMR) AF: 0.764 AC: 7683 AN: 10058

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 1920 AN: 2617

East Asian (EAS) AF: 0.647 AC: 2258 AN: 3490

South Asian (SAS) AF: 0.761 AC: 1902 AN: 2498

European-Finnish (FIN) AF: 0.693 AC: 3872 AN: 5586

Middle Eastern (MID) AF: 0.665 AC: 143 AN: 215

European-Non Finnish (NFE) AF: 0.825 AC: 43439 AN: 52635

Other (OTH) AF: 0.653 AC: 968 AN: 1482

Alfa AF: 0.745 Hom.: 31203

Bravo AF: 0.632

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.7
DANN	Benign	0.91
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs239748; hg19: chrX-18883358;