X-8391136-T-C

Variant names:

• chrX-8391136-T-C
• rs1534255
• ENST00000746116.1:n.72-29951T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000746116.1(ENSG00000285679):​n.72-29951T>C 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 110,728 control chromosomes in the GnomAD database, including 3,579 homozygotes. There are 9,524 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 (3579 hom., 9524 hem., cov: 22)
• Consequence: ENSG00000285679 ENST00000746116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 1 publications found

Genes affected

ENSG00000285679 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746116.1. 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
	ENSG00000285679	ENST00000746116.1		n.72-29951T>C		intron	N/A
	ENSG00000285679	ENST00000746117.1		n.72-34141T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.294 AC: 32537 AN: 110676 Hom.: 3579 Cov.: 22

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.294 AC: 32556 AN: 110728 Hom.: 3579 Cov.: 22 AF XY: 0.289 AC XY: 9524 AN XY: 32990

African (AFR) AF: 0.343 AC: 10436 AN: 30468

American (AMR) AF: 0.281 AC: 2916 AN: 10359

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 563 AN: 2640

East Asian (EAS) AF: 0.491 AC: 1696 AN: 3457

South Asian (SAS) AF: 0.274 AC: 723 AN: 2638

European-Finnish (FIN) AF: 0.311 AC: 1810 AN: 5824

Middle Eastern (MID) AF: 0.167 AC: 36 AN: 216

European-Non Finnish (NFE) AF: 0.261 AC: 13807 AN: 52938

Other (OTH) AF: 0.285 AC: 430 AN: 1511

Alfa AF: 0.272 Hom.: 21383

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.49
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1534255; hg19: chrX-8359177;