ENST00000813769.1:n.506-13136A>G

Variant names:

• chr3-30354459-T-C
• rs11129399
• ENST00000813769.1:n.506-13136A>G

Variant summary

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

The ENST00000813769.1(ENSG00000227549):​n.506-13136A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,094 control chromosomes in the GnomAD database, including 1,651 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 0.12 (1651 hom., cov: 32)
• Consequence: ENSG00000227549 ENST00000813769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 5 publications found

Genes affected

ENSG00000227549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927995	XR_427323.4	n.1149+3520T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227549	ENST00000813769.1	n.506-13136A>G		intron_variant	Intron 5 of 5
ENSG00000289450	ENST00000813894.1	n.240+3520T>C		intron_variant	Intron 1 of 3
ENSG00000289450	ENST00000813896.1	n.222+3520T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17504 AN: 151974 Hom.: 1645 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0422

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.115 AC: 17527 AN: 152094 Hom.: 1651 Cov.: 32 AF XY: 0.118 AC XY: 8755 AN XY: 74340

African (AFR) AF: 0.247 AC: 10255 AN: 41462

American (AMR) AF: 0.0901 AC: 1377 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1078 AN: 5152

South Asian (SAS) AF: 0.166 AC: 799 AN: 4818

European-Finnish (FIN) AF: 0.0442 AC: 469 AN: 10610

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0422 AC: 2866 AN: 67988

Other (OTH) AF: 0.101 AC: 214 AN: 2110

Alfa AF: 0.0682 Hom.: 2650

Bravo AF: 0.125

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.73
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs11129399; hg19: chr3-30395951;