ENST00000792147.1:n.331-15257A>C

Variant names:

• chr3-36350218-T-G
• rs1842149
• ENST00000792147.1:n.331-15257A>C

Variant summary

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

The ENST00000792147.1(ENSG00000303138):​n.331-15257A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,080 control chromosomes in the GnomAD database, including 56,438 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 0.86 (56438 hom., cov: 30)
• Consequence: ENSG00000303138 ENST00000792147.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 3 publications found

Genes affected

ENSG00000303138 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792147.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303138	ENST00000792147.1		n.331-15257A>C		intron	N/A
	ENSG00000303138	ENST00000792148.1		n.143-12358A>C		intron	N/A
	ENSG00000303138	ENST00000792149.1		n.115-12358A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130897 AN: 151962 Hom.: 56396 Cov.: 30

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.861 AC: 130997 AN: 152080 Hom.: 56438 Cov.: 30 AF XY: 0.863 AC XY: 64175 AN XY: 74332

African (AFR) AF: 0.845 AC: 35051 AN: 41462

American (AMR) AF: 0.861 AC: 13140 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3062 AN: 3472

East Asian (EAS) AF: 0.989 AC: 5117 AN: 5172

South Asian (SAS) AF: 0.880 AC: 4243 AN: 4820

European-Finnish (FIN) AF: 0.877 AC: 9281 AN: 10582

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58200 AN: 67994

Other (OTH) AF: 0.852 AC: 1802 AN: 2116

Alfa AF: 0.857 Hom.: 47053

Bravo AF: 0.860

Asia WGS AF: 0.931 AC: 3238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.52
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1842149; hg19: chr3-36391710;