X-142363531-T-C

Variant names:

• chrX-142363531-T-C
• rs5908293
• ENST00000664519.1:n.369-19521T>C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000664519.1(ENSG00000288098):​n.369-19521T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.74 (21522 hom., 23585 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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
ENSG00000288098	ENST00000664519.1	n.369-19521T>C		intron_variant	Intron 3 of 9

Frequencies

GnomAD3 genomes AF: 0.742 AC: 81275 AN: 109581 Hom.: 21528 Cov.: 22 AF XY: 0.739 AC XY: 23538 AN XY: 31837

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.748

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: 0.742 AC: 81303 AN: 109628 Hom.: 21522 Cov.: 22 AF XY: 0.739 AC XY: 23585 AN XY: 31896

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.739

Alfa AF: 0.728 Hom.: 57728

Bravo AF: 0.743

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.16
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5908293; hg19: chrX-141451317;