rs584589

Positions:

• chr17-49486191-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.0974

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.0942

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.136

Alfa AF: 0.143 Hom.: 2247

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs584589; hg19: chr17-47563553;