rs1353456

Variant names:

• chrX-79687224-C-A
• rs1353456

Your query was ambiguous. Multiple possible variants found:

• chrX-79687224-C-A
• chrX-79687224-C-T

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 0.63 (17218 hom., 20833 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• 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=-0.8).

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: 0.627 AC: 69417 AN: 110686 Hom.: 17228 Cov.: 24

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.672

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: 0.627 AC: 69419 AN: 110738 Hom.: 17218 Cov.: 24 AF XY: 0.631 AC XY: 20833 AN XY: 33002

African (AFR) AF: 0.283 AC: 8648 AN: 30546

American (AMR) AF: 0.569 AC: 5914 AN: 10394

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2181 AN: 2640

East Asian (EAS) AF: 0.627 AC: 2175 AN: 3470

South Asian (SAS) AF: 0.860 AC: 2281 AN: 2652

European-Finnish (FIN) AF: 0.762 AC: 4450 AN: 5838

Middle Eastern (MID) AF: 0.817 AC: 174 AN: 213

European-Non Finnish (NFE) AF: 0.795 AC: 41996 AN: 52821

Other (OTH) AF: 0.673 AC: 1000 AN: 1486

Alfa AF: 0.721 Hom.: 34164

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.9
DANN	Benign	0.63
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1353456; hg19: chrX-78942721;