rs10521430

Variant names:

• chrX-43427013-T-C
• rs10521430
• ENST00000649774.1:n.619-11322T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649774.1(ENSG00000285899):​n.619-11322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 111,952 control chromosomes in the GnomAD database, including 41 homozygotes. There are 691 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 0.021 (41 hom., 691 hem., cov: 23)
• Consequence: ENSG00000285899 ENST00000649774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

Genes affected

ENSG00000285899 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.066 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
ENSG00000285899	ENST00000649774.1	n.619-11322T>C		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.0209 AC: 2335 AN: 111895 Hom.: 40 Cov.: 23 AF XY: 0.0202 AC XY: 689 AN XY: 34053

Gnomad AFR AF: 0.00426

Gnomad AMI AF: 0.00291

Gnomad AMR AF: 0.0699

Gnomad ASJ AF: 0.0238

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00862

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0217

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0209 AC: 2340 AN: 111952 Hom.: 41 Cov.: 23 AF XY: 0.0203 AC XY: 691 AN XY: 34120

Gnomad4 AFR AF: 0.00425

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.0238

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00901

Gnomad4 FIN AF: 0.0307

Gnomad4 NFE AF: 0.0217

Gnomad4 OTH AF: 0.0236

Alfa AF: 0.0241 Hom.: 203

Bravo AF: 0.0251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521430; hg19: chrX-43286262;