rs9549447

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819056.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306489	ENST00000819056.1		n.1120G>A		non_coding_transcript_exon	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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9549447;

hg19: chr13-112835240;