ENST00000752965.1:n.766A>G

Variant names:

• chr3-179288845-T-C
• rs9290675
• ENST00000752965.1:n.766A>G

Variant summary

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

The ENST00000752965.1(ENSG00000298104):​n.766A>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 0.0947 in 152,284 control chromosomes in the GnomAD database, including 726 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 0.095 (726 hom., cov: 32)
• Consequence: ENSG00000298104 ENST00000752965.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 8 publications found

Genes affected

ENSG00000298104 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.095 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
ENSG00000298104	ENST00000752965.1	n.766A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0948 AC: 14423 AN: 152166 Hom.: 727 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0948

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.0794

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.0947 AC: 14425 AN: 152284 Hom.: 726 Cov.: 32 AF XY: 0.0950 AC XY: 7074 AN XY: 74472

African (AFR) AF: 0.0941 AC: 3909 AN: 41560

American (AMR) AF: 0.0947 AC: 1448 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3472

East Asian (EAS) AF: 0.00675 AC: 35 AN: 5188

South Asian (SAS) AF: 0.0797 AC: 385 AN: 4830

European-Finnish (FIN) AF: 0.0951 AC: 1010 AN: 10618

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.0969 AC: 6592 AN: 68004

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.0897 Hom.: 605

Bravo AF: 0.0968

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.3
DANN	Benign	0.77
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs9290675; hg19: chr3-179006633;