ENST00000466706.2:n.-27C>T

Variant names:

• chr6-132633824-G-A
• rs7739700
• ENST00000466706.2:n.-27C>T

Variant summary

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

The ENST00000466706.2(ENSG00000290584):​n.-27C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,988 control chromosomes in the GnomAD database, including 9,212 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 0.34 (9212 hom., cov: 31)
• Consequence: ENSG00000290584 ENST00000466706.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 5 publications found

Genes affected

ENSG00000290584 (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 = 0.454 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
ENSG00000290584	ENST00000466706.2	n.-27C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51499 AN: 151872 Hom.: 9208 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.339 AC: 51533 AN: 151988 Hom.: 9212 Cov.: 31 AF XY: 0.341 AC XY: 25343 AN XY: 74274

African (AFR) AF: 0.237 AC: 9823 AN: 41458

American (AMR) AF: 0.314 AC: 4797 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1154 AN: 3472

East Asian (EAS) AF: 0.470 AC: 2425 AN: 5162

South Asian (SAS) AF: 0.376 AC: 1810 AN: 4814

European-Finnish (FIN) AF: 0.380 AC: 4009 AN: 10562

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.387 AC: 26302 AN: 67936

Other (OTH) AF: 0.329 AC: 696 AN: 2114

Alfa AF: 0.271 Hom.: 1148

Bravo AF: 0.328

Asia WGS AF: 0.401 AC: 1391 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	0.84
DANN	Benign	0.74
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7739700; hg19: chr6-132954963; COSMIC: COSV58605478;