chrX-142260444-C-G

Variant names:

• chrX-142260444-C-G
• rs10521814
• ENST00000664519.1:n.368+36345C>G

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.368+36345C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 111,636 control chromosomes in the GnomAD database, including 774 homozygotes. There are 4,162 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 0.13 (774 hom., 4162 hem., cov: 23)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 0 publications found

Genes affected

ENSG00000288098 (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 = 0.182 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
ENSG00000288098	ENST00000664519.1	n.368+36345C>G		intron_variant	Intron 3 of 9

Frequencies

GnomAD3 genomes AF: 0.131 AC: 14579 AN: 111581 Hom.: 775 Cov.: 23

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0586

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00393

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0675

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.131 AC: 14610 AN: 111636 Hom.: 774 Cov.: 23 AF XY: 0.123 AC XY: 4162 AN XY: 33888

African (AFR) AF: 0.186 AC: 5711 AN: 30733

American (AMR) AF: 0.0745 AC: 785 AN: 10535

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 370 AN: 2647

East Asian (EAS) AF: 0.00394 AC: 14 AN: 3552

South Asian (SAS) AF: 0.0380 AC: 103 AN: 2713

European-Finnish (FIN) AF: 0.113 AC: 688 AN: 6087

Middle Eastern (MID) AF: 0.0694 AC: 15 AN: 216

European-Non Finnish (NFE) AF: 0.126 AC: 6694 AN: 52945

Other (OTH) AF: 0.125 AC: 190 AN: 1525

Alfa AF: 0.130 Hom.: 706

Bravo AF: 0.130

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.45
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs10521814; hg19: chrX-141348230;