ENST00000664519.1:n.369-19521T>C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -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

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

African (AFR) AF: 0.770 AC: 23192 AN: 30122

American (AMR) AF: 0.754 AC: 7695 AN: 10203

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 1909 AN: 2619

East Asian (EAS) AF: 0.601 AC: 2066 AN: 3439

South Asian (SAS) AF: 0.718 AC: 1815 AN: 2529

European-Finnish (FIN) AF: 0.760 AC: 4322 AN: 5685

Middle Eastern (MID) AF: 0.748 AC: 160 AN: 214

European-Non Finnish (NFE) AF: 0.732 AC: 38564 AN: 52666

Other (OTH) AF: 0.739 AC: 1093 AN: 1479

Alfa AF: 0.734 Hom.: 80434

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
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs5908293; hg19: chrX-141451317;