rs1573906

Variant names:

• chrX-86880585-T-C
• rs1573906
• ENST00000804502.1:n.153+25876A>G

Variant summary

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

The ENST00000804502.1(ENSG00000304551):​n.153+25876A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 111,002 control chromosomes in the GnomAD database, including 1,100 homozygotes. There are 4,769 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 0.15 (1100 hom., 4769 hem., cov: 23)
• Consequence: ENSG00000304551 ENST00000804502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 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
ENSG00000304551	ENST00000804502.1	n.153+25876A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.147 AC: 16337 AN: 110952 Hom.: 1096 Cov.: 23

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0556

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.147 AC: 16351 AN: 111002 Hom.: 1100 Cov.: 23 AF XY: 0.143 AC XY: 4769 AN XY: 33436

African (AFR) AF: 0.180 AC: 5520 AN: 30727

American (AMR) AF: 0.307 AC: 3171 AN: 10335

Ashkenazi Jewish (ASJ) AF: 0.0685 AC: 181 AN: 2644

East Asian (EAS) AF: 0.0778 AC: 274 AN: 3523

South Asian (SAS) AF: 0.164 AC: 448 AN: 2737

European-Finnish (FIN) AF: 0.109 AC: 644 AN: 5910

Middle Eastern (MID) AF: 0.133 AC: 28 AN: 211

European-Non Finnish (NFE) AF: 0.110 AC: 5808 AN: 52716

Other (OTH) AF: 0.158 AC: 239 AN: 1516

Alfa AF: 0.132 Hom.: 1236

Bravo AF: 0.169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.4
DANN	Benign	0.53
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1573906; hg19: chrX-86135588;