X-122971702-A-T

Variant names:

• chrX-122971702-A-T
• rs1293524

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 0.90 (31586 hom., 28708 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• 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=-0.93).

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: 0.897 AC: 98532 AN: 109833 Hom.: 31593 Cov.: 22

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.957

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.894

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: 0.897 AC: 98579 AN: 109884 Hom.: 31586 Cov.: 22 AF XY: 0.894 AC XY: 28708 AN XY: 32104

African (AFR) AF: 0.940 AC: 28359 AN: 30166

American (AMR) AF: 0.815 AC: 8422 AN: 10336

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 2503 AN: 2630

East Asian (EAS) AF: 0.579 AC: 1986 AN: 3428

South Asian (SAS) AF: 0.860 AC: 2173 AN: 2527

European-Finnish (FIN) AF: 0.905 AC: 5194 AN: 5741

Middle Eastern (MID) AF: 0.957 AC: 202 AN: 211

European-Non Finnish (NFE) AF: 0.907 AC: 47792 AN: 52679

Other (OTH) AF: 0.891 AC: 1325 AN: 1487

Alfa AF: 0.897 Hom.: 7935

Bravo AF: 0.890

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		0.014

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: rs1293524;

hg19: chrX-122105555;