X-142040246-G-T

Variant names:

• chrX-142040246-G-T
• rs2207272
• ENST00000664519.1:n.222+105529G>T

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.222+105529G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 110,079 control chromosomes in the GnomAD database, including 3,954 homozygotes. There are 9,508 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 0.29 (3954 hom., 9508 hem., cov: 22)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 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.222+105529G>T		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.294 AC: 32365 AN: 110028 Hom.: 3959 Cov.: 22 AF XY: 0.293 AC XY: 9488 AN XY: 32344

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.294 AC: 32377 AN: 110079 Hom.: 3954 Cov.: 22 AF XY: 0.293 AC XY: 9508 AN XY: 32405

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.354

Alfa AF: 0.344 Hom.: 29637

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2207272; hg19: chrX-141128032;