chr12-52889414-C-A

Variant names:

• chr12-52889414-C-A
• rs1907671

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 0.471 in 151,966 control chromosomes in the GnomAD database, including 17,568 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 0.47 (17568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.885
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 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: 0.472 AC: 71597 AN: 151848 Hom.: 17555 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.471 AC: 71644 AN: 151966 Hom.: 17568 Cov.: 32 AF XY: 0.475 AC XY: 35304 AN XY: 74258

African (AFR) AF: 0.336 AC: 13921 AN: 41444

American (AMR) AF: 0.535 AC: 8173 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1886 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3161 AN: 5160

South Asian (SAS) AF: 0.704 AC: 3399 AN: 4826

European-Finnish (FIN) AF: 0.429 AC: 4518 AN: 10522

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34779 AN: 67960

Other (OTH) AF: 0.492 AC: 1036 AN: 2106

Alfa AF: 0.503 Hom.: 74251

Bravo AF: 0.474

Asia WGS AF: 0.580 AC: 2017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.3
DANN	Benign	0.56
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs1907671; hg19: chr12-53283198;