ENST00000770012.1:n.-65G>T

Variant names:

• chr9-118597268-C-A
• rs11789407
• ENST00000770012.1:n.-65G>T

Variant summary

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

The ENST00000770012.1(ENSG00000300201):​n.-65G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,976 control chromosomes in the GnomAD database, including 14,949 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 0.43 (14949 hom., cov: 32)
• Consequence: ENSG00000300201 ENST00000770012.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 8 publications found

Genes affected

ENSG00000300201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770012.1. 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
	ENSG00000300201	ENST00000770012.1		n.-65G>T		upstream_gene	N/A
	ENSG00000300201	ENST00000770013.1		n.-62G>T		upstream_gene	N/A
	ENSG00000300201	ENST00000770014.1		n.-15G>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65682 AN: 151858 Hom.: 14937 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.433 AC: 65736 AN: 151976 Hom.: 14949 Cov.: 32 AF XY: 0.428 AC XY: 31763 AN XY: 74280

African (AFR) AF: 0.341 AC: 14122 AN: 41472

American (AMR) AF: 0.396 AC: 6043 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2209 AN: 3466

East Asian (EAS) AF: 0.166 AC: 859 AN: 5168

South Asian (SAS) AF: 0.282 AC: 1353 AN: 4806

European-Finnish (FIN) AF: 0.505 AC: 5335 AN: 10560

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34250 AN: 67932

Other (OTH) AF: 0.460 AC: 970 AN: 2110

Alfa AF: 0.458 Hom.: 2817

Bravo AF: 0.420

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.74
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs11789407; hg19: chr9-121359546;