rs10813797

Variant names:

• chr9-32359193-C-A
• rs10813797
• ENST00000785072.1:n.286-10989C>A

Variant summary

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

The ENST00000785072.1(ENSG00000302224):​n.286-10989C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,956 control chromosomes in the GnomAD database, including 10,763 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 0.36 (10763 hom., cov: 32)
• Consequence: ENSG00000302224 ENST00000785072.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 2 publications found

Genes affected

ENSG00000302224 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 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
ENSG00000302224	ENST00000785072.1	n.286-10989C>A		intron_variant	Intron 2 of 2
ENSG00000302224	ENST00000785073.1	n.158-11028C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55325 AN: 151840 Hom.: 10760 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.364 AC: 55341 AN: 151956 Hom.: 10763 Cov.: 32 AF XY: 0.362 AC XY: 26849 AN XY: 74260

African (AFR) AF: 0.231 AC: 9579 AN: 41472

American (AMR) AF: 0.411 AC: 6257 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1376 AN: 5178

South Asian (SAS) AF: 0.330 AC: 1587 AN: 4806

European-Finnish (FIN) AF: 0.369 AC: 3884 AN: 10536

Middle Eastern (MID) AF: 0.441 AC: 128 AN: 290

European-Non Finnish (NFE) AF: 0.442 AC: 30012 AN: 67938

Other (OTH) AF: 0.377 AC: 798 AN: 2116

Alfa AF: 0.419 Hom.: 7484

Bravo AF: 0.360

Asia WGS AF: 0.309 AC: 1070 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10813797; hg19: chr9-32359191;