13-28649857-C-T

Variant names:

• chr13-28649857-C-T
• rs9550386
• ENST00000784142.1:n.114+9120G>A

Variant summary

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

The ENST00000784142.1(ENSG00000289569):​n.114+9120G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,060 control chromosomes in the GnomAD database, including 1,932 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 0.16 (1932 hom., cov: 32)
• Consequence: ENSG00000289569 ENST00000784142.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.755
• Publications: 1 publications found

Genes affected

ENSG00000289569 (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 (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784142.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289569	ENST00000784142.1		n.114+9120G>A		intron	N/A
	ENSG00000289569	ENST00000784143.1		n.102+9120G>A		intron	N/A
	ENSG00000289569	ENST00000784144.1		n.102+9120G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23861 AN: 151942 Hom.: 1931 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0953

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.157 AC: 23871 AN: 152060 Hom.: 1932 Cov.: 32 AF XY: 0.157 AC XY: 11636 AN XY: 74318

African (AFR) AF: 0.154 AC: 6403 AN: 41494

American (AMR) AF: 0.166 AC: 2539 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0953 AC: 331 AN: 3472

East Asian (EAS) AF: 0.193 AC: 998 AN: 5162

South Asian (SAS) AF: 0.231 AC: 1111 AN: 4816

European-Finnish (FIN) AF: 0.118 AC: 1241 AN: 10538

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10769 AN: 67982

Other (OTH) AF: 0.138 AC: 290 AN: 2108

Alfa AF: 0.152 Hom.: 3079

Bravo AF: 0.159

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.42
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs9550386; hg19: chr13-29223994;