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).

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: 0.897 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 v4.3

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

Other links and lift over

dbSNP: rs1293524; hg19: chrX-122105555;