rs10521804

chrX-140944242-T-C

Variant summary

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

The ENST00000413328.1(ENSG00000229269):n.123+12382T>C variant causes a intron, non coding transcript 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: ENST00000413328.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000413328.1	n.123+12382T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 7684 AN: 112242 Hom.: 333 Cov.: 24 AF XY: 0.0638 AC XY: 2195 AN XY: 34396

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

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0567

Gnomad4 ASJ AF: 0.0249

Gnomad4 EAS AF: 0.00837

Gnomad4 SAS AF: 0.0590

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.0350

Gnomad4 OTH AF: 0.0571

Alfa AF: 0.0554 Hom.: 404

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521804; hg19: chrX-140026407;