rs162486

Variant names:

• chr5-123737784-A-G
• rs162486

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 0.171 in 151,984 control chromosomes in the GnomAD database, including 2,360 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 0.17 (2360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 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: 0.171 AC: 25987 AN: 151866 Hom.: 2355 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0935

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.171 AC: 25989 AN: 151984 Hom.: 2360 Cov.: 32 AF XY: 0.165 AC XY: 12274 AN XY: 74318

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0933

Gnomad4 SAS AF: 0.0821

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.178

Alfa AF: 0.178 Hom.: 290

Bravo AF: 0.173

Asia WGS AF: 0.0790 AC: 274 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs162486; hg19: chr5-123073478;