rs6530125

Variant names:

• chrX-7983228-G-A
• rs6530125
• ENST00000655333.1:n.469-34828G>A

Variant summary

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

The ENST00000655333.1(ENSG00000285679):​n.469-34828G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 111,342 control chromosomes in the GnomAD database, including 1,539 homozygotes. There are 3,681 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 0.12 (1539 hom., 3681 hem., cov: 23)
• Consequence: ENSG00000285679 ENST00000655333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796
• Publications: 0 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655333.1. 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	ENST00000655333.1		n.469-34828G>A		intron	N/A
	ENSG00000285679	ENST00000659022.1		n.971+53815G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.119 AC: 13231 AN: 111294 Hom.: 1540 Cov.: 23

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0554

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.00780

Gnomad FIN AF: 0.00330

Gnomad MID AF: 0.0798

Gnomad NFE AF: 0.00741

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.119 AC: 13229 AN: 111342 Hom.: 1539 Cov.: 23 AF XY: 0.109 AC XY: 3681 AN XY: 33650

African (AFR) AF: 0.356 AC: 10871 AN: 30498

American (AMR) AF: 0.142 AC: 1481 AN: 10459

Ashkenazi Jewish (ASJ) AF: 0.0554 AC: 146 AN: 2634

East Asian (EAS) AF: 0.0323 AC: 115 AN: 3558

South Asian (SAS) AF: 0.00746 AC: 20 AN: 2682

European-Finnish (FIN) AF: 0.00330 AC: 20 AN: 6063

Middle Eastern (MID) AF: 0.0783 AC: 17 AN: 217

European-Non Finnish (NFE) AF: 0.00741 AC: 393 AN: 53022

Other (OTH) AF: 0.109 AC: 166 AN: 1522

Alfa AF: 0.0803 Hom.: 604

Bravo AF: 0.143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs6530125; hg19: chrX-7951269;