rs1606355

Variant names:

• chr12-28662859-G-A
• rs1606355

Your query was ambiguous. Multiple possible variants found:

• chr12-28662859-G-A
• chr12-28662859-G-C
• chr12-28662859-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 0.809 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;