X-142100668-C-T

Position:

• chrX-142100668-C-T

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.223-95039C>T 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 0.92 (33233 hom., 30088 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENST00000664519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664519.1	n.223-95039C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.922 AC: 101753 AN: 110377 Hom.: 33244 Cov.: 23 AF XY: 0.921 AC XY: 30039 AN XY: 32607

Gnomad AFR AF: 0.822

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.975

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.944

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.918

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: 0.922 AC: 101783 AN: 110428 Hom.: 33233 Cov.: 23 AF XY: 0.921 AC XY: 30088 AN XY: 32668

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.965

Gnomad4 ASJ AF: 0.975

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.968

Gnomad4 OTH AF: 0.912

Alfa AF: 0.956 Hom.: 56359

Bravo AF: 0.920

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2206118; hg19: chrX-141188454;