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).

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: 0.544 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 v4.3

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

Other links and lift over

dbSNP: rs2159767; hg19: chrX-147381021;