rs1463865

Variant names:

• chr12-130166709-G-A
• rs1463865

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 0.302 in 152,024 control chromosomes in the GnomAD database, including 7,654 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 0.30 (7654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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 (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.302 AC: 45802 AN: 151906 Hom.: 7630 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.302 AC: 45863 AN: 152024 Hom.: 7654 Cov.: 32 AF XY: 0.309 AC XY: 22944 AN XY: 74306

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.284

Alfa AF: 0.270 Hom.: 1170

Bravo AF: 0.297

Asia WGS AF: 0.568 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463865; hg19: chr12-130651254;