rs1533317

Variant names:

• chr4-35409009-T-C
• rs1533317
• ENST00000743803.1:n.322+2262T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-35409009-T-C
• chr4-35409009-T-G

Variant summary

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

The ENST00000743803.1(ENSG00000296945):​n.322+2262T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,008 control chromosomes in the GnomAD database, including 17,108 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 0.44 (17108 hom., cov: 32)
• Consequence: ENSG00000296945 ENST00000743803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 10 publications found

Genes affected

ENSG00000296945 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 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
ENSG00000296945	ENST00000743803.1	n.322+2262T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66867 AN: 151890 Hom.: 17111 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.440 AC: 66871 AN: 152008 Hom.: 17108 Cov.: 32 AF XY: 0.443 AC XY: 32941 AN XY: 74286

African (AFR) AF: 0.164 AC: 6812 AN: 41524

American (AMR) AF: 0.534 AC: 8139 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1872 AN: 3468

East Asian (EAS) AF: 0.565 AC: 2913 AN: 5154

South Asian (SAS) AF: 0.512 AC: 2464 AN: 4810

European-Finnish (FIN) AF: 0.484 AC: 5112 AN: 10558

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37834 AN: 67932

Other (OTH) AF: 0.476 AC: 1004 AN: 2108

Alfa AF: 0.522 Hom.: 71215

Bravo AF: 0.431

Asia WGS AF: 0.523 AC: 1817 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.63
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1533317; hg19: chr4-35410631;