rs12612420

Variant names:

• chr2-200293399-G-A
• rs12612420

Your query was ambiguous. Multiple possible variants found:

• chr2-200293399-G-A
• chr2-200293399-G-T

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 0.141 in 151,846 control chromosomes in the GnomAD database, including 1,885 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 0.14 (1885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 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: 0.142 AC: 21473 AN: 151728 Hom.: 1886 Cov.: 32

Gnomad AFR AF: 0.0466

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.141 AC: 21460 AN: 151846 Hom.: 1885 Cov.: 32 AF XY: 0.144 AC XY: 10699 AN XY: 74150

African (AFR) AF: 0.0464 AC: 1924 AN: 41444

American (AMR) AF: 0.118 AC: 1796 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1132 AN: 5158

South Asian (SAS) AF: 0.335 AC: 1605 AN: 4784

European-Finnish (FIN) AF: 0.150 AC: 1574 AN: 10522

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11957 AN: 67964

Other (OTH) AF: 0.156 AC: 328 AN: 2102

Alfa AF: 0.167 Hom.: 7264

Bravo AF: 0.130

Asia WGS AF: 0.254 AC: 880 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.41
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs12612420; hg19: chr2-201158122;