13-97507450-T-C

Variant names:

• chr13-97507450-T-C
• rs9513249
• ENST00000802609.1:n.309-13857A>G

Variant summary

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

The ENST00000802609.1(ENSG00000304344):​n.309-13857A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 152,052 control chromosomes in the GnomAD database, including 37,325 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 0.69 (37325 hom., cov: 31)
• Consequence: ENSG00000304344 ENST00000802609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 4 publications found

Genes affected

ENSG00000304344 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.754 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
ENSG00000304344	ENST00000802609.1	n.309-13857A>G		intron_variant	Intron 2 of 2
ENSG00000304344	ENST00000802610.1	n.376-13857A>G		intron_variant	Intron 3 of 3
ENSG00000304344	ENST00000802611.1	n.712-4909A>G		intron_variant	Intron 4 of 4
ENSG00000304344	ENST00000802612.1	n.376-4909A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105298 AN: 151932 Hom.: 37305 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.693 AC: 105360 AN: 152052 Hom.: 37325 Cov.: 31 AF XY: 0.692 AC XY: 51457 AN XY: 74326

African (AFR) AF: 0.561 AC: 23280 AN: 41464

American (AMR) AF: 0.745 AC: 11382 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2844 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2190 AN: 5152

South Asian (SAS) AF: 0.764 AC: 3675 AN: 4808

European-Finnish (FIN) AF: 0.731 AC: 7737 AN: 10582

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51631 AN: 67982

Other (OTH) AF: 0.736 AC: 1551 AN: 2108

Alfa AF: 0.745 Hom.: 139571

Bravo AF: 0.684

Asia WGS AF: 0.589 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.42
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs9513249; hg19: chr13-98159704;