rs9510428

Variant names:

• chr13-22925194-G-A
• rs9510428
• ENST00000832883.1:n.158C>T

Variant summary

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

The ENST00000832883.1(ENSG00000308260):​n.158C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,128 control chromosomes in the GnomAD database, including 49,419 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 0.80 (49419 hom., cov: 32)
• Consequence: ENSG00000308260 ENST00000832883.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 3 publications found

Genes affected

ENSG00000308260 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 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
ENSG00000308260	ENST00000832883.1	n.158C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308260	ENST00000832882.1	n.516-148C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121692 AN: 152010 Hom.: 49399 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.800 AC: 121754 AN: 152128 Hom.: 49419 Cov.: 32 AF XY: 0.806 AC XY: 59987 AN XY: 74384

African (AFR) AF: 0.648 AC: 26874 AN: 41446

American (AMR) AF: 0.850 AC: 12996 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2848 AN: 3470

East Asian (EAS) AF: 0.881 AC: 4547 AN: 5160

South Asian (SAS) AF: 0.851 AC: 4108 AN: 4826

European-Finnish (FIN) AF: 0.931 AC: 9873 AN: 10606

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57874 AN: 68016

Other (OTH) AF: 0.795 AC: 1676 AN: 2108

Alfa AF: 0.820 Hom.: 19728

Bravo AF: 0.790

Asia WGS AF: 0.846 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.32
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9510428; hg19: chr13-23499333;