3-30440818-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927995	XR_001740627.2	n.213-28215C>T		intron_variant	Intron 3 of 3
LOC101927995	XR_001740628.2	n.261-28215C>T		intron_variant	Intron 4 of 4
LOC101927995	XR_007095856.1	n.257-28215C>T		intron_variant	Intron 4 of 4
LOC105377013	XR_940683.2	n.293+189G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289450	ENST00000691186.2	n.282-28215C>T		intron_variant	Intron 3 of 3
ENSG00000227549	ENST00000813769.1	n.399-18452G>A		intron_variant	Intron 4 of 5
ENSG00000289450	ENST00000813894.1	n.392-28215C>T		intron_variant	Intron 3 of 3
ENSG00000289450	ENST00000813895.1	n.225-28215C>T		intron_variant	Intron 3 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs13073411; hg19: chr3-30482310;