12-7303001-A-G

Variant names:

• chr12-7303001-A-G
• rs7137120
• ENST00000767257.1:n.*171T>C

Variant summary

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

The ENST00000767257.1(ENSG00000299889):​n.*171T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,062 control chromosomes in the GnomAD database, including 52,192 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 0.83 (52192 hom., cov: 31)
• Consequence: ENSG00000299889 ENST00000767257.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 3 publications found

Genes affected

ENSG00000299889 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 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
ENSG00000299889	ENST00000767257.1	n.*171T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125726 AN: 151944 Hom.: 52163 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.827 AC: 125815 AN: 152062 Hom.: 52192 Cov.: 31 AF XY: 0.825 AC XY: 61297 AN XY: 74312

African (AFR) AF: 0.798 AC: 33100 AN: 41460

American (AMR) AF: 0.816 AC: 12461 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2891 AN: 3468

East Asian (EAS) AF: 0.913 AC: 4722 AN: 5174

South Asian (SAS) AF: 0.717 AC: 3450 AN: 4812

European-Finnish (FIN) AF: 0.841 AC: 8887 AN: 10570

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57677 AN: 67984

Other (OTH) AF: 0.824 AC: 1736 AN: 2108

Alfa AF: 0.836 Hom.: 34027

Bravo AF: 0.823

Asia WGS AF: 0.827 AC: 2875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.44
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7137120; hg19: chr12-7455597;