rs1606355

Positions:

• chr12-28662859-G-A

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 0.809 in 151,770 control chromosomes in the GnomAD database, including 50,010 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 0.81 (50010 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.836 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: 0.809 AC: 122726 AN: 151652 Hom.: 49979 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.809 AC: 122815 AN: 151770 Hom.: 50010 Cov.: 31 AF XY: 0.807 AC XY: 59815 AN XY: 74136

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.820

Alfa AF: 0.819 Hom.: 6340

Bravo AF: 0.798

Asia WGS AF: 0.691 AC: 2402 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1606355; hg19: chr12-28815792;