ENST00000789342.1:n.115-288G>A

Variant names:

• chr12-63154276-C-T
• rs7308855
• ENST00000789342.1:n.115-288G>A

Variant summary

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

The ENST00000789342.1(ENSG00000302754):​n.115-288G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0849 in 152,268 control chromosomes in the GnomAD database, including 609 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 0.085 (609 hom., cov: 33)
• Consequence: ENSG00000302754 ENST00000789342.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 4 publications found

Genes affected

ENSG00000302754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.104 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
ENSG00000302754	ENST00000789342.1	n.115-288G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12920 AN: 152150 Hom.: 609 Cov.: 33

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.0745

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

GnomAD4 genome AF: 0.0849 AC: 12928 AN: 152268 Hom.: 609 Cov.: 33 AF XY: 0.0841 AC XY: 6262 AN XY: 74464

African (AFR) AF: 0.0677 AC: 2811 AN: 41550

American (AMR) AF: 0.0718 AC: 1099 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0746 AC: 259 AN: 3472

East Asian (EAS) AF: 0.0384 AC: 199 AN: 5182

South Asian (SAS) AF: 0.112 AC: 540 AN: 4824

European-Finnish (FIN) AF: 0.0866 AC: 918 AN: 10602

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0992 AC: 6747 AN: 68014

Other (OTH) AF: 0.0737 AC: 156 AN: 2116

Alfa AF: 0.0885 Hom.: 909

Bravo AF: 0.0799

Asia WGS AF: 0.0750 AC: 260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.46
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs7308855; hg19: chr12-63548056;