rs12085366

Variant names:

• chr1-198447874-T-C
• rs12085366
• ENST00000792155.1:n.188-1487T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000792155.1(ENSG00000303141):​n.188-1487T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,854 control chromosomes in the GnomAD database, including 1,999 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 0.16 (1999 hom., cov: 30)
• Consequence: ENSG00000303141 ENST00000792155.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 3 publications found

Genes affected

ENSG00000303141 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792155.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303141	ENST00000792155.1		n.188-1487T>C		intron	N/A
	ENSG00000303141	ENST00000792156.1		n.242-1487T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23915 AN: 151736 Hom.: 1996 Cov.: 30

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.158 AC: 23934 AN: 151854 Hom.: 1999 Cov.: 30 AF XY: 0.163 AC XY: 12087 AN XY: 74232

African (AFR) AF: 0.131 AC: 5428 AN: 41466

American (AMR) AF: 0.177 AC: 2696 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 473 AN: 3456

East Asian (EAS) AF: 0.325 AC: 1675 AN: 5158

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4812

European-Finnish (FIN) AF: 0.201 AC: 2114 AN: 10542

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10094 AN: 67894

Other (OTH) AF: 0.167 AC: 352 AN: 2104

Alfa AF: 0.149 Hom.: 502

Bravo AF: 0.153

Asia WGS AF: 0.298 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.19
DANN	Benign	0.39
PhyloP100		-0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12085366;

hg19: chr1-198417004;