rs3783557

Variant names:

• chr2-112773135-C-T
• rs3783557
• ENST00000762706.1:n.404+2239C>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+2239C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,928 control chromosomes in the GnomAD database, including 4,094 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 0.20 (4094 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38
• Publications: 9 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 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+2239C>T		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.499+2239C>T		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.265+2239C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30782 AN: 151810 Hom.: 4094 Cov.: 31

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.0309

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.203 AC: 30780 AN: 151928 Hom.: 4094 Cov.: 31 AF XY: 0.202 AC XY: 14994 AN XY: 74252

African (AFR) AF: 0.0522 AC: 2164 AN: 41470

American (AMR) AF: 0.165 AC: 2517 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1077 AN: 3468

East Asian (EAS) AF: 0.0311 AC: 161 AN: 5174

South Asian (SAS) AF: 0.206 AC: 992 AN: 4810

European-Finnish (FIN) AF: 0.315 AC: 3318 AN: 10518

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19646 AN: 67914

Other (OTH) AF: 0.214 AC: 453 AN: 2112

Alfa AF: 0.236 Hom.: 1034

Bravo AF: 0.183

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.094
DANN	Benign	0.42
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs3783557; hg19: chr2-113530712;