X-142040246-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664519.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288098	ENST00000664519.1		n.222+105529G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.294 AC: 32365 AN: 110028 Hom.: 3959 Cov.: 22

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

African (AFR) AF: 0.132 AC: 4023 AN: 30376

American (AMR) AF: 0.457 AC: 4696 AN: 10267

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 993 AN: 2622

East Asian (EAS) AF: 0.517 AC: 1760 AN: 3407

South Asian (SAS) AF: 0.409 AC: 1040 AN: 2543

European-Finnish (FIN) AF: 0.310 AC: 1799 AN: 5804

Middle Eastern (MID) AF: 0.387 AC: 82 AN: 212

European-Non Finnish (NFE) AF: 0.328 AC: 17308 AN: 52693

Other (OTH) AF: 0.354 AC: 524 AN: 1481

Alfa AF: 0.334 Hom.: 33646

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2207272;

hg19: chrX-141128032;