rs5954635

Variant names:

• chrX-142363056-A-G
• rs5954635
• ENST00000664519.1:n.369-19996A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000664519.1(ENSG00000288098):​n.369-19996A>G 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 0.72 (20225 hom., 23057 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 3 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=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664519.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288098	ENST00000664519.1		n.369-19996A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 78945 AN: 109918 Hom.: 20232 Cov.: 22

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.727

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: 0.718 AC: 78974 AN: 109971 Hom.: 20225 Cov.: 22 AF XY: 0.715 AC XY: 23057 AN XY: 32249

African (AFR) AF: 0.764 AC: 23115 AN: 30237

American (AMR) AF: 0.734 AC: 7514 AN: 10234

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 1885 AN: 2629

East Asian (EAS) AF: 0.601 AC: 2071 AN: 3447

South Asian (SAS) AF: 0.715 AC: 1816 AN: 2539

European-Finnish (FIN) AF: 0.701 AC: 4023 AN: 5742

Middle Eastern (MID) AF: 0.755 AC: 163 AN: 216

European-Non Finnish (NFE) AF: 0.698 AC: 36826 AN: 52749

Other (OTH) AF: 0.718 AC: 1078 AN: 1502

Alfa AF: 0.704 Hom.: 27003

Bravo AF: 0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.31
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs5954635; hg19: chrX-141450842;