rs918582

Variant names:

• chr5-58882943-G-A
• rs918582

Your query was ambiguous. Multiple possible variants found:

• chr5-58882943-G-A
• chr5-58882943-G-C
• chr5-58882943-G-T

Variant summary

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

The variant allele was found at a frequency of 0.329 in 151,928 control chromosomes in the GnomAD database, including 8,761 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 0.33 (8761 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.329 AC: 49979 AN: 151810 Hom.: 8751 Cov.: 33

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.329 AC: 50030 AN: 151928 Hom.: 8761 Cov.: 33 AF XY: 0.331 AC XY: 24566 AN XY: 74282

African (AFR) AF: 0.435 AC: 18039 AN: 41424

American (AMR) AF: 0.338 AC: 5153 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3468

East Asian (EAS) AF: 0.487 AC: 2516 AN: 5168

South Asian (SAS) AF: 0.323 AC: 1552 AN: 4812

European-Finnish (FIN) AF: 0.298 AC: 3141 AN: 10536

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17862 AN: 67948

Other (OTH) AF: 0.287 AC: 607 AN: 2112

Alfa AF: 0.275 Hom.: 2991

Bravo AF: 0.337

Asia WGS AF: 0.398 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs918582; hg19: chr5-58178770;