rs584589

Variant names:

• chr17-49486191-A-G
• rs584589
• ENST00000832581.1:n.296T>C

Variant summary

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

The ENST00000832581.1(ENSG00000308220):​n.296T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,230 control chromosomes in the GnomAD database, including 1,613 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 0.14 (1613 hom., cov: 33)
• Consequence: ENSG00000308220 ENST00000832581.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 5 publications found

Genes affected

ENSG00000308220 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 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
ENSG00000308220	ENST00000832581.1	n.296T>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000308220	ENST00000832582.1	n.296T>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000308220	ENST00000832585.1	n.296T>C		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21215 AN: 152112 Hom.: 1608 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.0941

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.139 AC: 21233 AN: 152230 Hom.: 1613 Cov.: 33 AF XY: 0.138 AC XY: 10273 AN XY: 74420

African (AFR) AF: 0.150 AC: 6225 AN: 41544

American (AMR) AF: 0.0974 AC: 1490 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3468

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5176

South Asian (SAS) AF: 0.0942 AC: 454 AN: 4822

European-Finnish (FIN) AF: 0.173 AC: 1834 AN: 10604

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9995 AN: 67994

Other (OTH) AF: 0.136 AC: 288 AN: 2112

Alfa AF: 0.142 Hom.: 5290

Bravo AF: 0.134

Asia WGS AF: 0.0640 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.9
DANN	Benign	0.84
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs584589; hg19: chr17-47563553;