12-89332648-C-G

Position:

• chr12-89332648-C-G

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 0.128 in 152,150 control chromosomes in the GnomAD database, including 1,929 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 (1929 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19390 AN: 152032 Hom.: 1925 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0740

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0797

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.128 AC: 19425 AN: 152150 Hom.: 1929 Cov.: 31 AF XY: 0.122 AC XY: 9111 AN XY: 74382

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.0739

Gnomad4 ASJ AF: 0.0685

Gnomad4 EAS AF: 0.00656

Gnomad4 SAS AF: 0.0749

Gnomad4 FIN AF: 0.0358

Gnomad4 NFE AF: 0.0797

Gnomad4 OTH AF: 0.108

Alfa AF: 0.119 Hom.: 177

Bravo AF: 0.136

Asia WGS AF: 0.0570 AC: 200 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12302525; hg19: chr12-89726425;