chr12-89314937-C-A

Position:

• chr12-89314937-C-A

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 0.561 in 151,746 control chromosomes in the GnomAD database, including 24,235 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 0.56 (24235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

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 (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85041 AN: 151628 Hom.: 24218 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.561 AC: 85081 AN: 151746 Hom.: 24235 Cov.: 32 AF XY: 0.556 AC XY: 41238 AN XY: 74126

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.553

Alfa AF: 0.578 Hom.: 34167

Bravo AF: 0.541

Asia WGS AF: 0.461 AC: 1605 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	3.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1688545; hg19: chr12-89708714;