rs1820460

Variant names:

• chr12-107310928-C-A
• rs1820460

Your query was ambiguous. Multiple possible variants found:

• chr12-107310928-C-A
• chr12-107310928-C-G

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 0.226 in 152,016 control chromosomes in the GnomAD database, including 4,346 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 0.23 (4346 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 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: 0.226 AC: 34376 AN: 151894 Hom.: 4341 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.226 AC: 34413 AN: 152016 Hom.: 4346 Cov.: 32 AF XY: 0.231 AC XY: 17192 AN XY: 74290

African (AFR) AF: 0.161 AC: 6673 AN: 41500

American (AMR) AF: 0.271 AC: 4147 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3470

East Asian (EAS) AF: 0.559 AC: 2869 AN: 5136

South Asian (SAS) AF: 0.297 AC: 1429 AN: 4810

European-Finnish (FIN) AF: 0.239 AC: 2517 AN: 10540

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14691 AN: 67964

Other (OTH) AF: 0.244 AC: 514 AN: 2110

Alfa AF: 0.225 Hom.: 13136

Bravo AF: 0.233

Asia WGS AF: 0.447 AC: 1551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.81
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1820460; hg19: chr12-107704705;