rs3783521

Variant names:

• chr2-112786000-G-A
• rs3783521
• ENST00000762706.1:n.404+15104G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-112786000-G-A
• chr2-112786000-G-C
• chr2-112786000-G-T

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+15104G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,142 control chromosomes in the GnomAD database, including 7,090 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 0.27 (7090 hom., cov: 33)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 22 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299339	ENST00000762706.1	n.404+15104G>A		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.499+15104G>A		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.265+15104G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41049 AN: 152024 Hom.: 7074 Cov.: 33

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.270 AC: 41078 AN: 152142 Hom.: 7090 Cov.: 33 AF XY: 0.280 AC XY: 20807 AN XY: 74378

African (AFR) AF: 0.0867 AC: 3598 AN: 41510

American (AMR) AF: 0.381 AC: 5820 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3468

East Asian (EAS) AF: 0.706 AC: 3655 AN: 5176

South Asian (SAS) AF: 0.311 AC: 1501 AN: 4824

European-Finnish (FIN) AF: 0.403 AC: 4258 AN: 10566

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20454 AN: 67988

Other (OTH) AF: 0.286 AC: 605 AN: 2114

Alfa AF: 0.250 Hom.: 1027

Bravo AF: 0.267

Asia WGS AF: 0.469 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.7
DANN	Benign	0.80
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs3783521; hg19: chr2-113543577; COSMIC: COSV54519187;