X-135463627-T-C

Variant names:

• chrX-135463627-T-C
• rs4320696

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 0.56 (12639 hom., 18670 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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: 0.565 AC: 62798 AN: 111206 Hom.: 12631 Cov.: 23

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.461

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.533

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: 0.565 AC: 62816 AN: 111261 Hom.: 12639 Cov.: 23 AF XY: 0.557 AC XY: 18670 AN XY: 33497

African (AFR) AF: 0.557 AC: 17066 AN: 30627

American (AMR) AF: 0.644 AC: 6802 AN: 10557

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1402 AN: 2629

East Asian (EAS) AF: 0.482 AC: 1680 AN: 3488

South Asian (SAS) AF: 0.386 AC: 1035 AN: 2683

European-Finnish (FIN) AF: 0.530 AC: 3152 AN: 5949

Middle Eastern (MID) AF: 0.464 AC: 98 AN: 211

European-Non Finnish (NFE) AF: 0.573 AC: 30332 AN: 52909

Other (OTH) AF: 0.538 AC: 824 AN: 1532

Alfa AF: 0.568 Hom.: 4492

Bravo AF: 0.576

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.66
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs4320696; hg19: chrX-134597552;