rs1606355

Variant names:

• chr12-28662859-G-A
• rs1606355
• ENST00000849941.1:n.46+34973C>T

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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000849941.1(ENSG00000310456):​n.46+34973C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000310456 ENST00000849941.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 1 publications found

Genes affected

ENSG00000310456 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000310456	ENST00000849941.1	n.46+34973C>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.801 AC: 33242 AN: 41492

American (AMR) AF: 0.774 AC: 11761 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2976 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2576 AN: 5140

South Asian (SAS) AF: 0.773 AC: 3716 AN: 4810

European-Finnish (FIN) AF: 0.830 AC: 8777 AN: 10574

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57024 AN: 67774

Other (OTH) AF: 0.820 AC: 1726 AN: 2104

Alfa AF: 0.818 Hom.: 6584

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
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1606355; hg19: chr12-28815792;