rs10521594

Variant names:

• chrX-8439288-C-A
• rs10521594
• ENST00000746116.1:n.225-540C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-8439288-C-A
• chrX-8439288-C-T

Variant summary

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

The ENST00000746116.1(ENSG00000285679):​n.225-540C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 109,562 control chromosomes in the GnomAD database, including 3,018 homozygotes. There are 8,256 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 0.27 (3018 hom., 8256 hem., cov: 22)
• Consequence: ENSG00000285679 ENST00000746116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 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.225-540C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.271 AC: 29731 AN: 109513 Hom.: 3020 Cov.: 22

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.271 AC: 29731 AN: 109562 Hom.: 3018 Cov.: 22 AF XY: 0.259 AC XY: 8256 AN XY: 31858

African (AFR) AF: 0.214 AC: 6472 AN: 30245

American (AMR) AF: 0.354 AC: 3588 AN: 10131

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 912 AN: 2633

East Asian (EAS) AF: 0.189 AC: 658 AN: 3479

South Asian (SAS) AF: 0.196 AC: 501 AN: 2560

European-Finnish (FIN) AF: 0.231 AC: 1297 AN: 5622

Middle Eastern (MID) AF: 0.393 AC: 83 AN: 211

European-Non Finnish (NFE) AF: 0.295 AC: 15507 AN: 52528

Other (OTH) AF: 0.289 AC: 429 AN: 1482

Alfa AF: 0.267 Hom.: 8317

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.43
PhyloP100		-0.24

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: rs10521594;

hg19: chrX-8407329;