ENST00000760115.1:n.347G>A

Variant names:

• chr18-79395184-G-A
• rs9962479
• ENST00000760115.1:n.347G>A

Variant summary

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

The ENST00000760115.1(ENSG00000299053):​n.347G>A 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 0.392 in 151,970 control chromosomes in the GnomAD database, including 13,242 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 0.39 (13242 hom., cov: 32)
• Consequence: ENSG00000299053 ENST00000760115.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788
• Publications: 10 publications found

Genes affected

ENSG00000299053 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 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
ENSG00000299053	ENST00000760115.1	n.347G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59578 AN: 151852 Hom.: 13238 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.392 AC: 59597 AN: 151970 Hom.: 13242 Cov.: 32 AF XY: 0.388 AC XY: 28836 AN XY: 74270

African (AFR) AF: 0.209 AC: 8662 AN: 41484

American (AMR) AF: 0.431 AC: 6597 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1616 AN: 3470

East Asian (EAS) AF: 0.111 AC: 565 AN: 5106

South Asian (SAS) AF: 0.291 AC: 1400 AN: 4818

European-Finnish (FIN) AF: 0.489 AC: 5182 AN: 10588

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34114 AN: 67902

Other (OTH) AF: 0.418 AC: 880 AN: 2106

Alfa AF: 0.462 Hom.: 28506

Bravo AF: 0.381

Asia WGS AF: 0.232 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.97
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs9962479; hg19: chr18-77155184;