3-13514336-C-T

Variant names:

• chr3-13514336-C-T
• rs2597513
• ENST00000752926.1:n.-94G>A

Variant summary

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

The ENST00000752926.1(ENSG00000298100):​n.-94G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,172 control chromosomes in the GnomAD database, including 59,235 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 0.88 (59235 hom., cov: 31)
• Consequence: ENSG00000298100 ENST00000752926.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 44 publications found

Genes affected

ENSG00000298100 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
ENSG00000298100	ENST00000752926.1	n.-94G>A		upstream_gene_variant
ENSG00000298100	ENST00000752927.1	n.-144G>A		upstream_gene_variant
ENSG00000298100	ENST00000752928.1	n.-165G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133987 AN: 152054 Hom.: 59187 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.881 AC: 134092 AN: 152172 Hom.: 59235 Cov.: 31 AF XY: 0.883 AC XY: 65664 AN XY: 74390

African (AFR) AF: 0.820 AC: 34043 AN: 41502

American (AMR) AF: 0.901 AC: 13787 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3003 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5167 AN: 5170

South Asian (SAS) AF: 0.949 AC: 4569 AN: 4816

European-Finnish (FIN) AF: 0.913 AC: 9684 AN: 10602

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60861 AN: 67996

Other (OTH) AF: 0.877 AC: 1853 AN: 2112

Alfa AF: 0.892 Hom.: 162939

Bravo AF: 0.876

Asia WGS AF: 0.960 AC: 3340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.1
DANN	Benign	0.77
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2597513; hg19: chr3-13555836;