ENST00000819056.1:n.1120G>A

Variant names:

• chr13-112180926-C-T
• rs9549447
• ENST00000819056.1:n.1120G>A

Variant summary

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

The ENST00000819056.1(ENSG00000306489):​n.1120G>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 0.372 in 152,076 control chromosomes in the GnomAD database, including 12,558 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 0.37 (12558 hom., cov: 34)
• Consequence: ENSG00000306489 ENST00000819056.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 3 publications found

Genes affected

ENSG00000306489 (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 (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370370	XR_944282.1	n.2364G>A		non_coding_transcript_exon_variant	Exon 6 of 6
LOC105370370	XR_944283.1	n.1299G>A		non_coding_transcript_exon_variant	Exon 7 of 7
LOC105370370	XR_944284.1	n.2004G>A		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306489	ENST00000819056.1	n.1120G>A		non_coding_transcript_exon_variant	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56607 AN: 151958 Hom.: 12550 Cov.: 34

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.372 AC: 56639 AN: 152076 Hom.: 12558 Cov.: 34 AF XY: 0.367 AC XY: 27265 AN XY: 74318

African (AFR) AF: 0.168 AC: 6952 AN: 41498

American (AMR) AF: 0.382 AC: 5833 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1706 AN: 3472

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5174

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4822

European-Finnish (FIN) AF: 0.478 AC: 5045 AN: 10556

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34249 AN: 67954

Other (OTH) AF: 0.395 AC: 831 AN: 2106

Alfa AF: 0.458 Hom.: 52347

Bravo AF: 0.357

Asia WGS AF: 0.177 AC: 620 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	4.0
DANN	Benign	0.72
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs9549447; hg19: chr13-112835240;