ENST00000834078.1:n.306-236G>A

Variant names:

• chr2-5377390-G-A
• rs792065
• ENST00000834078.1:n.306-236G>A

Variant summary

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

The ENST00000834078.1(ENSG00000308446):​n.306-236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,122 control chromosomes in the GnomAD database, including 4,819 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 0.23 (4819 hom., cov: 33)
• Consequence: ENSG00000308446 ENST00000834078.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

Genes affected

ENSG00000308446 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 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
ENSG00000308446	ENST00000834078.1	n.306-236G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35289 AN: 152004 Hom.: 4819 Cov.: 33

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.232 AC: 35288 AN: 152122 Hom.: 4819 Cov.: 33 AF XY: 0.234 AC XY: 17390 AN XY: 74342

African (AFR) AF: 0.0888 AC: 3685 AN: 41516

American (AMR) AF: 0.270 AC: 4136 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 848 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2275 AN: 5150

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4822

European-Finnish (FIN) AF: 0.238 AC: 2514 AN: 10566

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19585 AN: 67990

Other (OTH) AF: 0.246 AC: 520 AN: 2112

Alfa AF: 0.270 Hom.: 3688

Bravo AF: 0.227

Asia WGS AF: 0.314 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.79
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs792065; hg19: chr2-5517523;