rs3829364

Variant names:

• chr13-37600396-T-C
• rs3829364
• ENST00000744989.1:n.48+3359T>C

Your query was ambiguous. Multiple possible variants found:

• chr13-37600396-T-C
• chr13-37600396-T-G

Variant summary

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

The ENST00000744989.1(ENSG00000297050):​n.48+3359T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,040 control chromosomes in the GnomAD database, including 794 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 0.087 (794 hom., cov: 32)
• Consequence: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 4 publications found

Genes affected

ENSG00000297050 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 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
ENSG00000297050	ENST00000744989.1	n.48+3359T>C		intron_variant	Intron 1 of 4
ENSG00000297050	ENST00000744990.1	n.70+3359T>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13157 AN: 151922 Hom.: 792 Cov.: 32

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0865 AC: 13155 AN: 152040 Hom.: 794 Cov.: 32 AF XY: 0.0866 AC XY: 6442 AN XY: 74350

African (AFR) AF: 0.0222 AC: 922 AN: 41548

American (AMR) AF: 0.0884 AC: 1345 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3472

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5178

South Asian (SAS) AF: 0.165 AC: 797 AN: 4816

European-Finnish (FIN) AF: 0.0912 AC: 966 AN: 10590

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

European-Non Finnish (NFE) AF: 0.122 AC: 8267 AN: 67908

Other (OTH) AF: 0.102 AC: 216 AN: 2108

Alfa AF: 0.107 Hom.: 559

Bravo AF: 0.0826

Asia WGS AF: 0.0730 AC: 254 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.72
DANN	Benign	0.41
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs3829364; hg19: chr13-38174533;