chr12-96905586-A-G

Variant names:

• chr12-96905586-A-G
• rs2024490

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.966 AC: 40150 AN: 41558

American (AMR) AF: 0.933 AC: 14275 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3255 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4995 AN: 5182

South Asian (SAS) AF: 0.886 AC: 4276 AN: 4826

European-Finnish (FIN) AF: 0.934 AC: 9916 AN: 10620

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60402 AN: 68020

Other (OTH) AF: 0.916 AC: 1937 AN: 2114

Alfa AF: 0.897 Hom.: 102144

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2024490; hg19: chr12-97299364;