X-142100668-C-T

Variant names:

• chrX-142100668-C-T
• rs2206118
• ENST00000664519.1:n.223-95039C>T

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.223-95039C>T 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 0.92 (33233 hom., 30088 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772
• 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=-0.96).

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.223-95039C>T		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.922 AC: 101753 AN: 110377 Hom.: 33244 Cov.: 23

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

African (AFR) AF: 0.822 AC: 24917 AN: 30329

American (AMR) AF: 0.965 AC: 9946 AN: 10310

Ashkenazi Jewish (ASJ) AF: 0.975 AC: 2564 AN: 2630

East Asian (EAS) AF: 0.925 AC: 3201 AN: 3461

South Asian (SAS) AF: 0.798 AC: 2058 AN: 2578

European-Finnish (FIN) AF: 0.970 AC: 5647 AN: 5824

Middle Eastern (MID) AF: 0.943 AC: 200 AN: 212

European-Non Finnish (NFE) AF: 0.968 AC: 51192 AN: 52893

Other (OTH) AF: 0.912 AC: 1375 AN: 1508

Alfa AF: 0.947 Hom.: 86249

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
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs2206118; hg19: chrX-141188454;