rs13073411

Variant names:

• chr3-30440818-C-T
• rs13073411
• ENST00000691186.2:n.282-28215C>T

Variant summary

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

The ENST00000691186.2(ENSG00000289450):​n.282-28215C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,128 control chromosomes in the GnomAD database, including 1,906 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 0.15 (1906 hom., cov: 32)
• Consequence: ENSG00000289450 ENST00000691186.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 4 publications found

Genes affected

ENSG00000289450 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691186.2. 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
	ENSG00000289450	ENST00000691186.2		n.282-28215C>T		intron	N/A
	ENSG00000227549	ENST00000813769.1		n.399-18452G>A		intron	N/A
	ENSG00000289450	ENST00000813894.1		n.392-28215C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23144 AN: 152010 Hom.: 1907 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.152 AC: 23147 AN: 152128 Hom.: 1906 Cov.: 32 AF XY: 0.152 AC XY: 11318 AN XY: 74360

African (AFR) AF: 0.127 AC: 5254 AN: 41494

American (AMR) AF: 0.108 AC: 1657 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3466

East Asian (EAS) AF: 0.104 AC: 537 AN: 5182

South Asian (SAS) AF: 0.155 AC: 749 AN: 4826

European-Finnish (FIN) AF: 0.196 AC: 2072 AN: 10580

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11504 AN: 67990

Other (OTH) AF: 0.167 AC: 353 AN: 2114

Alfa AF: 0.168 Hom.: 7107

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.71
PhyloP100		-0.12

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: rs13073411;

hg19: chr3-30482310;