ENST00000789342.1:n.115-324A>G

Variant names:

• chr12-63154312-T-C
• rs7294536
• ENST00000789342.1:n.115-324A>G

Variant summary

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

The ENST00000789342.1(ENSG00000302754):​n.115-324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,124 control chromosomes in the GnomAD database, including 7,717 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 0.26 (7717 hom., cov: 33)
• Consequence: ENSG00000302754 ENST00000789342.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765
• Publications: 9 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 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.115-324A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39096 AN: 152004 Hom.: 7694 Cov.: 33

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0864

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.257 AC: 39160 AN: 152124 Hom.: 7717 Cov.: 33 AF XY: 0.254 AC XY: 18894 AN XY: 74380

African (AFR) AF: 0.550 AC: 22805 AN: 41448

American (AMR) AF: 0.153 AC: 2333 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0864 AC: 300 AN: 3472

East Asian (EAS) AF: 0.148 AC: 768 AN: 5178

South Asian (SAS) AF: 0.278 AC: 1336 AN: 4814

European-Finnish (FIN) AF: 0.141 AC: 1495 AN: 10598

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9375 AN: 68002

Other (OTH) AF: 0.216 AC: 457 AN: 2112

Alfa AF: 0.201 Hom.: 622

Bravo AF: 0.265

Asia WGS AF: 0.256 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs7294536; hg19: chr12-63548092;