rs12386481

Variant names:

• chr5-180406485-G-A
• rs12386481

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 0.514 in 151,924 control chromosomes in the GnomAD database, including 21,962 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 0.51 (21962 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.63 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: 0.514 AC: 78066 AN: 151806 Hom.: 21953 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.514 AC: 78090 AN: 151924 Hom.: 21962 Cov.: 32 AF XY: 0.514 AC XY: 38141 AN XY: 74268

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.519

Alfa AF: 0.596 Hom.: 15656

Bravo AF: 0.496

Asia WGS AF: 0.494 AC: 1713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12386481; hg19: chr5-179833485;