rs1896086

Variant names:

• chr12-108029663-A-G
• rs1896086

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 0.129 in 152,074 control chromosomes in the GnomAD database, including 3,172 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 0.13 (3172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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: 0.129 AC: 19554 AN: 151952 Hom.: 3156 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.00848

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00221

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.129 AC: 19616 AN: 152074 Hom.: 3172 Cov.: 32 AF XY: 0.129 AC XY: 9624 AN XY: 74348

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.00375

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.00848

Gnomad4 NFE AF: 0.00221

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0468 Hom.: 361

Bravo AF: 0.151

Asia WGS AF: 0.194 AC: 672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	17
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1896086; hg19: chr12-108423440;