12-52892714-G-C

Variant names:

• chr12-52892714-G-C
• rs4300473

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 0.455 in 152,018 control chromosomes in the GnomAD database, including 16,247 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 0.45 (16247 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 2 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 = 0.67 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: 0.455 AC: 69097 AN: 151900 Hom.: 16234 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.455 AC: 69144 AN: 152018 Hom.: 16247 Cov.: 32 AF XY: 0.459 AC XY: 34091 AN XY: 74280

African (AFR) AF: 0.351 AC: 14544 AN: 41452

American (AMR) AF: 0.513 AC: 7832 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1743 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3173 AN: 5176

South Asian (SAS) AF: 0.690 AC: 3324 AN: 4818

European-Finnish (FIN) AF: 0.398 AC: 4200 AN: 10544

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32624 AN: 67970

Other (OTH) AF: 0.470 AC: 994 AN: 2114

Alfa AF: 0.298 Hom.: 715

Bravo AF: 0.459

Asia WGS AF: 0.574 AC: 1997 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	0.28
DANN	Benign	0.48
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs4300473; hg19: chr12-53286498;