chrX-142363056-A-G

Position:

• chrX-142363056-A-G

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.369-19996A>G variant causes a intron, non coding transcript 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: ENST00000664519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664519.1	n.369-19996A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.718 AC: 78945 AN: 109918 Hom.: 20232 Cov.: 22 AF XY: 0.715 AC XY: 23008 AN XY: 32186

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

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.718

Alfa AF: 0.700 Hom.: 17355

Bravo AF: 0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5954635; hg19: chrX-141450842;