chrX-148299501-T-C

Variant names:

• chrX-148299501-T-C
• rs2159767

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 0.54 (12748 hom., 18234 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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: 0.544 AC: 60330 AN: 110955 Hom.: 12741 Cov.: 23

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.553

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: 0.544 AC: 60339 AN: 111009 Hom.: 12748 Cov.: 23 AF XY: 0.548 AC XY: 18234 AN XY: 33275

African (AFR) AF: 0.269 AC: 8235 AN: 30664

American (AMR) AF: 0.718 AC: 7518 AN: 10466

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1432 AN: 2648

East Asian (EAS) AF: 0.872 AC: 3040 AN: 3485

South Asian (SAS) AF: 0.521 AC: 1365 AN: 2622

European-Finnish (FIN) AF: 0.671 AC: 3903 AN: 5816

Middle Eastern (MID) AF: 0.595 AC: 128 AN: 215

European-Non Finnish (NFE) AF: 0.629 AC: 33285 AN: 52903

Other (OTH) AF: 0.555 AC: 838 AN: 1511

Alfa AF: 0.554 Hom.: 27836

Bravo AF: 0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.84
PhyloP100		-0.071

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2159767;

hg19: chrX-147381021;