rs585344

Variant names:

• chr18-50872497-G-A
• rs585344

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 0.321 in 152,028 control chromosomes in the GnomAD database, including 8,148 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 0.32 (8148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.677

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48784 AN: 151910 Hom.: 8143 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.321 AC: 48810 AN: 152028 Hom.: 8148 Cov.: 32 AF XY: 0.319 AC XY: 23686 AN XY: 74318

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.309

Alfa AF: 0.344 Hom.: 1167

Bravo AF: 0.309

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs585344; hg19: chr18-48398867; COSMIC: COSV69621494;