rs2619415

chr12-28000814-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0215

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.0920

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0696

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0739

Alfa AF: 0.103 Hom.: 221

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2619415; hg19: chr12-28153747;