17-5808630-A-G

Variant names:

• chr17-5808630-A-G
• rs1008588
• ENST00000573619.1:c.-523-28551A>G

Variant summary

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

The ENST00000573619.1(ENSG00000285471):​c.-523-28551A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,076 control chromosomes in the GnomAD database, including 15,677 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 0.41 (15677 hom., cov: 31)
• Consequence: ENSG00000285471 ENST00000573619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 14 publications found

Genes affected

ENSG00000285471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC339166	NR_040000.1	n.795-28551A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285471	ENST00000573619.1	c.-523-28551A>G		intron_variant	Intron 1 of 4	2		ENSP00000461865.1
ENSG00000284837	ENST00000563763.5	n.795-28551A>G		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62745 AN: 151958 Hom.: 15674 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.413 AC: 62760 AN: 152076 Hom.: 15677 Cov.: 31 AF XY: 0.413 AC XY: 30670 AN XY: 74326

African (AFR) AF: 0.123 AC: 5092 AN: 41514

American (AMR) AF: 0.512 AC: 7819 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1915 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1293 AN: 5156

South Asian (SAS) AF: 0.420 AC: 2022 AN: 4818

European-Finnish (FIN) AF: 0.535 AC: 5657 AN: 10568

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37353 AN: 67950

Other (OTH) AF: 0.438 AC: 926 AN: 2112

Alfa AF: 0.510 Hom.: 87097

Bravo AF: 0.398

Asia WGS AF: 0.354 AC: 1231 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.52
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1008588; hg19: chr17-5711950; COSMIC: COSV73784464;