rs162486

Positions:

• chr5-123737784-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 0.171 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;