rs13290397

Variant names:

• chr9-78768538-C-G
• rs13290397
• ENST00000761517.1:n.73-307C>G

Variant summary

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

The ENST00000761517.1(ENSG00000299197):​n.73-307C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,198 control chromosomes in the GnomAD database, including 1,113 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 0.11 (1113 hom., cov: 33)
• Consequence: ENSG00000299197 ENST00000761517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 2 publications found

Genes affected

ENSG00000299197 (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 (AFR) allele frequency at 95% confidence interval = 0.153 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
ENSG00000299197	ENST00000761517.1	n.73-307C>G		intron_variant	Intron 1 of 1
ENSG00000299220	ENST00000761645.1	n.379+6703G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17073 AN: 152080 Hom.: 1108 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0945

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

GnomAD4 genome AF: 0.112 AC: 17112 AN: 152198 Hom.: 1113 Cov.: 33 AF XY: 0.109 AC XY: 8086 AN XY: 74410

African (AFR) AF: 0.156 AC: 6481 AN: 41508

American (AMR) AF: 0.0578 AC: 883 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0613 AC: 213 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5190

South Asian (SAS) AF: 0.0447 AC: 215 AN: 4814

European-Finnish (FIN) AF: 0.116 AC: 1224 AN: 10590

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7776 AN: 68028

Other (OTH) AF: 0.0935 AC: 197 AN: 2106

Alfa AF: 0.117 Hom.: 136

Bravo AF: 0.108

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs13290397; hg19: chr9-81383454;