rs10522040

Variant names:

• chrX-36411364-C-T
• rs10522040
• ENST00000455438.2:n.1404+2551G>A

Variant summary

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

The ENST00000455438.2(ENSG00000226484):​n.1404+2551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 110,418 control chromosomes in the GnomAD database, including 3,600 homozygotes. There are 5,057 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 0.17 (3600 hom., 5057 hem., cov: 22)
• Consequence: ENSG00000226484 ENST00000455438.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 0 publications found

Genes affected

ENSG00000226484 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455438.2. 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
	LOC101928627	NR_110412.1		n.1404+2551G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226484	ENST00000455438.2	TSL:2	n.1404+2551G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 18794 AN: 110373 Hom.: 3599 Cov.: 22

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.0278

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.00228

Gnomad EAS AF: 0.00113

Gnomad SAS AF: 0.0467

Gnomad FIN AF: 0.00579

Gnomad MID AF: 0.0603

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.171 AC: 18839 AN: 110418 Hom.: 3600 Cov.: 22 AF XY: 0.154 AC XY: 5057 AN XY: 32760

African (AFR) AF: 0.563 AC: 17001 AN: 30189

American (AMR) AF: 0.0689 AC: 716 AN: 10389

Ashkenazi Jewish (ASJ) AF: 0.00228 AC: 6 AN: 2628

East Asian (EAS) AF: 0.00113 AC: 4 AN: 3533

South Asian (SAS) AF: 0.0472 AC: 123 AN: 2604

European-Finnish (FIN) AF: 0.00579 AC: 34 AN: 5870

Middle Eastern (MID) AF: 0.0613 AC: 13 AN: 212

European-Non Finnish (NFE) AF: 0.0140 AC: 738 AN: 52802

Other (OTH) AF: 0.123 AC: 185 AN: 1507

Alfa AF: 0.107 Hom.: 727

Bravo AF: 0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		0.14

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: rs10522040;

hg19: chrX-36429477;