12-96905586-A-G

Variant names:

• chr12-96905586-A-G
• rs2024490

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 0.921 in 152,290 control chromosomes in the GnomAD database, including 64,618 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 0.92 (64618 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 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: 0.921 AC: 140085 AN: 152172 Hom.: 64550 Cov.: 33

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.921 AC: 140213 AN: 152290 Hom.: 64618 Cov.: 33 AF XY: 0.922 AC XY: 68697 AN XY: 74472

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.916

Alfa AF: 0.894 Hom.: 79983

Bravo AF: 0.923

Asia WGS AF: 0.906 AC: 3152 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	1.7
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2024490; hg19: chr12-97299364;