X-87747441-A-G

Variant names:

• chrX-87747441-A-G
• rs5924105
• ENST00000635331.1:n.129+3314T>C

Variant summary

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

The ENST00000635331.1(ENSG00000282914):​n.129+3314T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.31 (6168 hom., 7800 hem., cov: 20)
• Consequence: ENSG00000282914 ENST00000635331.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 1 publications found

Genes affected

ENSG00000282914 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 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
ENSG00000282914	ENST00000635331.1	n.129+3314T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.307 AC: 32473 AN: 105905 Hom.: 6160 Cov.: 20

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.307 AC: 32513 AN: 105922 Hom.: 6168 Cov.: 20 AF XY: 0.267 AC XY: 7800 AN XY: 29176

African (AFR) AF: 0.670 AC: 18827 AN: 28110

American (AMR) AF: 0.297 AC: 2925 AN: 9833

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 493 AN: 2588

East Asian (EAS) AF: 0.543 AC: 1800 AN: 3317

South Asian (SAS) AF: 0.244 AC: 587 AN: 2410

European-Finnish (FIN) AF: 0.0906 AC: 474 AN: 5234

Middle Eastern (MID) AF: 0.156 AC: 32 AN: 205

European-Non Finnish (NFE) AF: 0.131 AC: 6843 AN: 52114

Other (OTH) AF: 0.276 AC: 401 AN: 1452

Alfa AF: 0.213 Hom.: 7401

Bravo AF: 0.358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.33
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs5924105; hg19: chrX-87002441;