ENST00000765690.1:n.1166C>G

Variant names:

• chr7-128208521-C-G
• rs2060736
• ENST00000765690.1:n.1166C>G

Variant summary

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

The ENST00000765690.1(ENSG00000292309):​n.1166C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,174 control chromosomes in the GnomAD database, including 47,343 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 0.78 (47343 hom., cov: 33)
• Consequence: ENSG00000292309 ENST00000765690.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 2 publications found

Genes affected

ENSG00000292309 (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 (EAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765690.1. 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
	ENSG00000292309	ENST00000765690.1		n.1166C>G		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000292309	ENST00000765691.1		n.1075C>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000292309	ENST00000765694.1		n.1263C>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118524 AN: 152058 Hom.: 47338 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.779 AC: 118560 AN: 152174 Hom.: 47343 Cov.: 33 AF XY: 0.780 AC XY: 58034 AN XY: 74396

African (AFR) AF: 0.598 AC: 24810 AN: 41470

American (AMR) AF: 0.745 AC: 11391 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2903 AN: 3472

East Asian (EAS) AF: 0.915 AC: 4737 AN: 5178

South Asian (SAS) AF: 0.770 AC: 3712 AN: 4820

European-Finnish (FIN) AF: 0.887 AC: 9397 AN: 10600

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

European-Non Finnish (NFE) AF: 0.866 AC: 58923 AN: 68020

Other (OTH) AF: 0.805 AC: 1698 AN: 2110

Alfa AF: 0.780 Hom.: 2602

Bravo AF: 0.761

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.47
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs2060736; hg19: chr7-127848574;