rs2619415

Variant names:

• chr12-28000814-G-T
• rs2619415

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 0.0836 in 152,142 control chromosomes in the GnomAD database, including 671 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 0.084 (671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 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: 0.0836 AC: 12714 AN: 152024 Hom.: 671 Cov.: 32

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.0920

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0696

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0836 AC: 12714 AN: 152142 Hom.: 671 Cov.: 32 AF XY: 0.0819 AC XY: 6091 AN XY: 74374

African (AFR) AF: 0.0215 AC: 894 AN: 41516

American (AMR) AF: 0.0761 AC: 1163 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0920 AC: 319 AN: 3466

East Asian (EAS) AF: 0.191 AC: 987 AN: 5158

South Asian (SAS) AF: 0.129 AC: 620 AN: 4810

European-Finnish (FIN) AF: 0.0696 AC: 737 AN: 10588

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7695 AN: 68002

Other (OTH) AF: 0.0739 AC: 156 AN: 2112

Alfa AF: 0.105 Hom.: 406

Bravo AF: 0.0824

Asia WGS AF: 0.137 AC: 477 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	3.4
DANN	Benign	0.71
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2619415; hg19: chr12-28153747;