rs9552680

Variant names:

• chr13-22661146-C-T
• rs9552680
• ENST00000815334.1:n.376+1740G>A

Variant summary

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

The ENST00000815334.1(ENSG00000306102):​n.376+1740G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,916 control chromosomes in the GnomAD database, including 8,170 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 0.33 (8170 hom., cov: 32)
• Consequence: ENSG00000306102 ENST00000815334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 6 publications found

Genes affected

ENSG00000306102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 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
ENSG00000306102	ENST00000815334.1	n.376+1740G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49507 AN: 151798 Hom.: 8165 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.326 AC: 49531 AN: 151916 Hom.: 8170 Cov.: 32 AF XY: 0.330 AC XY: 24491 AN XY: 74224

African (AFR) AF: 0.341 AC: 14133 AN: 41446

American (AMR) AF: 0.287 AC: 4377 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1715 AN: 5152

South Asian (SAS) AF: 0.380 AC: 1829 AN: 4814

European-Finnish (FIN) AF: 0.423 AC: 4459 AN: 10540

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21101 AN: 67938

Other (OTH) AF: 0.329 AC: 695 AN: 2110

Alfa AF: 0.311 Hom.: 1225

Bravo AF: 0.310

Asia WGS AF: 0.358 AC: 1248 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	0.84
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9552680; hg19: chr13-23235285;