ENST00000664519.1:n.223-129506A>G

Variant names:

• chrX-142066201-A-G
• rs2144096
• ENST00000664519.1:n.223-129506A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664519.1(ENSG00000288098):​n.223-129506A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 110,328 control chromosomes in the GnomAD database, including 5,148 homozygotes. There are 11,314 hemizygotes in GnomAD. 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 0.36 (5148 hom., 11314 hem., cov: 23)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

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.223-129506A>G		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.355 AC: 39152 AN: 110275 Hom.: 5151 Cov.: 23 AF XY: 0.346 AC XY: 11286 AN XY: 32657

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.395

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.355 AC: 39172 AN: 110328 Hom.: 5148 Cov.: 23 AF XY: 0.346 AC XY: 11314 AN XY: 32720

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.399

Alfa AF: 0.336 Hom.: 6232

Bravo AF: 0.372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2144096; hg19: chrX-141153987;