ENST00000664519.1:n.369-17680A>G

Variant names:

• chrX-142365372-A-G
• rs10521819
• ENST00000664519.1:n.369-17680A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000664519.1(ENSG00000288098):​n.369-17680A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00734 in 112,005 control chromosomes in the GnomAD database, including 11 homozygotes. There are 267 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 0.0073 (11 hom., 267 hem., cov: 24)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• 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=-0.82).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00734 (822/112005) while in subpopulation AMR AF = 0.0534 (559/10477). AF 95% confidence interval is 0.0497. There are 11 homozygotes in GnomAd4. There are 267 alleles in the male GnomAd4 subpopulation. Median coverage is 24. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 11 gene

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.369-17680A>G		intron_variant	Intron 3 of 9

Frequencies

GnomAD3 genomes AF: 0.00736 AC: 824 AN: 111957 Hom.: 11 Cov.: 24

Gnomad AFR AF: 0.00139

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0535

Gnomad ASJ AF: 0.00264

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00148

Gnomad FIN AF: 0.00344

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00342

Gnomad OTH AF: 0.00467

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

GnomAD4 genome AF: 0.00734 AC: 822 AN: 112005 Hom.: 11 Cov.: 24 AF XY: 0.00780 AC XY: 267 AN XY: 34213

African (AFR) AF: 0.00139 AC: 43 AN: 30944

American (AMR) AF: 0.0534 AC: 559 AN: 10477

Ashkenazi Jewish (ASJ) AF: 0.00264 AC: 7 AN: 2651

East Asian (EAS) AF: 0.00 AC: 0 AN: 3551

South Asian (SAS) AF: 0.00112 AC: 3 AN: 2690

European-Finnish (FIN) AF: 0.00344 AC: 21 AN: 6112

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 216

European-Non Finnish (NFE) AF: 0.00342 AC: 182 AN: 53162

Other (OTH) AF: 0.00462 AC: 7 AN: 1516

Alfa AF: 0.00696 Hom.: 29

Bravo AF: 0.0117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.42
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10521819; hg19: chrX-141453158;