rs10521804

Variant names:

• chrX-140944242-T-C
• rs10521804
• ENST00000413328.1:n.123+12382T>C

Variant summary

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

The ENST00000413328.1(ENSG00000229269):​n.123+12382T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0687 in 112,295 control chromosomes in the GnomAD database, including 336 homozygotes. There are 2,216 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 0.069 (336 hom., 2216 hem., cov: 24)
• Consequence: ENSG00000229269 ENST00000413328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710
• Publications: 0 publications found

Genes affected

ENSG00000229269 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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
ENSG00000229269	ENST00000413328.1	n.123+12382T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 7684 AN: 112242 Hom.: 333 Cov.: 24

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0249

Gnomad EAS AF: 0.00835

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.0333

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0687 AC: 7714 AN: 112295 Hom.: 336 Cov.: 24 AF XY: 0.0643 AC XY: 2216 AN XY: 34459

African (AFR) AF: 0.152 AC: 4710 AN: 30886

American (AMR) AF: 0.0567 AC: 599 AN: 10567

Ashkenazi Jewish (ASJ) AF: 0.0249 AC: 66 AN: 2648

East Asian (EAS) AF: 0.00837 AC: 30 AN: 3584

South Asian (SAS) AF: 0.0590 AC: 159 AN: 2695

European-Finnish (FIN) AF: 0.0123 AC: 76 AN: 6180

Middle Eastern (MID) AF: 0.0320 AC: 7 AN: 219

European-Non Finnish (NFE) AF: 0.0350 AC: 1864 AN: 53293

Other (OTH) AF: 0.0571 AC: 88 AN: 1542

Alfa AF: 0.0597 Hom.: 486

Bravo AF: 0.0786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.62
PhyloP100		0.71
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10521804; hg19: chrX-140026407;