rs576594

Variant names:

• chr9-95556929-A-G
• rs576594
• ENST00000810486.1:n.289+3924A>G

Variant summary

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

The ENST00000810486.1(ENSG00000305334):​n.289+3924A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,112 control chromosomes in the GnomAD database, including 35,054 homozygotes. 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 0.67 (35054 hom., cov: 32)
• Consequence: ENSG00000305334 ENST00000810486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 5 publications found

Genes affected

ENSG00000305334 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 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
ENSG00000305334	ENST00000810486.1	n.289+3924A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101855 AN: 151994 Hom.: 34985 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.670 AC: 101986 AN: 152112 Hom.: 35054 Cov.: 32 AF XY: 0.672 AC XY: 49957 AN XY: 74346

African (AFR) AF: 0.834 AC: 34630 AN: 41504

American (AMR) AF: 0.643 AC: 9825 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2093 AN: 3464

East Asian (EAS) AF: 0.680 AC: 3516 AN: 5172

South Asian (SAS) AF: 0.683 AC: 3300 AN: 4832

European-Finnish (FIN) AF: 0.654 AC: 6903 AN: 10558

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39669 AN: 67976

Other (OTH) AF: 0.642 AC: 1356 AN: 2112

Alfa AF: 0.607 Hom.: 121103

Bravo AF: 0.676

Asia WGS AF: 0.694 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.3
DANN	Benign	0.53
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs576594; hg19: chr9-98319211;