rs2858719

Variant names:

• chrX-86905129-C-A
• rs2858719
• ENST00000804502.1:n.153+1332G>T

Variant summary

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

The ENST00000804502.1(ENSG00000304551):​n.153+1332G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 109,803 control chromosomes in the GnomAD database, including 4,427 homozygotes. There are 8,912 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 (4427 hom., 8912 hem., cov: 22)
• Consequence: ENSG00000304551 ENST00000804502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 0 publications found

Genes affected

ENSG00000304551 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804502.1. 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
	ENSG00000304551	ENST00000804502.1		n.153+1332G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 31381 AN: 109763 Hom.: 4424 Cov.: 22

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.0617

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.286 AC: 31407 AN: 109803 Hom.: 4427 Cov.: 22 AF XY: 0.277 AC XY: 8912 AN XY: 32185

African (AFR) AF: 0.507 AC: 15289 AN: 30163

American (AMR) AF: 0.457 AC: 4687 AN: 10251

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 301 AN: 2618

East Asian (EAS) AF: 0.297 AC: 1028 AN: 3461

South Asian (SAS) AF: 0.266 AC: 688 AN: 2587

European-Finnish (FIN) AF: 0.160 AC: 912 AN: 5690

Middle Eastern (MID) AF: 0.215 AC: 45 AN: 209

European-Non Finnish (NFE) AF: 0.152 AC: 7995 AN: 52643

Other (OTH) AF: 0.280 AC: 420 AN: 1500

Alfa AF: 0.223 Hom.: 7570

Bravo AF: 0.325

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.64
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2858719; hg19: chrX-86160132;