chrX-24451605-G-A

Variant names:

• chrX-24451605-G-A
• rs10482283
• ENST00000730553.1:n.110-2942C>T

Variant summary

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

The ENST00000730553.1(ENSG00000295515):​n.110-2942C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 109,065 control chromosomes in the GnomAD database, including 5,528 homozygotes. There are 8,572 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 0.29 (5528 hom., 8572 hem., cov: 21)
• Consequence: ENSG00000295515 ENST00000730553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 3 publications found

Genes affected

ENSG00000295515 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730553.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295515	ENST00000730553.1		n.110-2942C>T		intron	N/A
	ENSG00000295515	ENST00000730554.1		n.116-2942C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.293 AC: 31896 AN: 109015 Hom.: 5524 Cov.: 21

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0897

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.293 AC: 31944 AN: 109065 Hom.: 5528 Cov.: 21 AF XY: 0.273 AC XY: 8572 AN XY: 31455

African (AFR) AF: 0.647 AC: 19241 AN: 29723

American (AMR) AF: 0.246 AC: 2519 AN: 10231

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 653 AN: 2621

East Asian (EAS) AF: 0.0894 AC: 309 AN: 3457

South Asian (SAS) AF: 0.230 AC: 572 AN: 2488

European-Finnish (FIN) AF: 0.134 AC: 768 AN: 5723

Middle Eastern (MID) AF: 0.197 AC: 42 AN: 213

European-Non Finnish (NFE) AF: 0.140 AC: 7362 AN: 52464

Other (OTH) AF: 0.278 AC: 408 AN: 1468

Alfa AF: 0.189 Hom.: 7530

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.068
DANN	Benign	0.56
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10482283; hg19: chrX-24469722;