ENST00000787151.1:n.880A>G

Variant names:

• chr13-27484267-A-G
• rs7336332
• ENST00000787151.1:n.880A>G

Variant summary

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

The ENST00000787151.1(ENSG00000302474):​n.880A>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 0.186 in 152,216 control chromosomes in the GnomAD database, including 3,069 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 0.19 (3069 hom., cov: 33)
• Consequence: ENSG00000302474 ENST00000787151.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 14 publications found

Genes affected

ENSG00000302474 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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
ENSG00000302474	ENST00000787151.1	n.880A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28282 AN: 152100 Hom.: 3061 Cov.: 33

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.186 AC: 28325 AN: 152216 Hom.: 3069 Cov.: 33 AF XY: 0.184 AC XY: 13680 AN XY: 74412

African (AFR) AF: 0.285 AC: 11837 AN: 41522

American (AMR) AF: 0.149 AC: 2277 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1069 AN: 5182

South Asian (SAS) AF: 0.0514 AC: 248 AN: 4828

European-Finnish (FIN) AF: 0.177 AC: 1875 AN: 10590

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10203 AN: 68012

Other (OTH) AF: 0.185 AC: 391 AN: 2114

Alfa AF: 0.155 Hom.: 4318

Bravo AF: 0.191

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.28
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs7336332; hg19: chr13-28058404;