rs13280813

Variant names:

• chr8-11567596-G-T
• rs13280813

Variant summary

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

The variant allele was found at a frequency of 0.347 in 152,064 control chromosomes in the GnomAD database, including 10,822 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 0.35 (10822 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 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

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52824 AN: 151946 Hom.: 10823 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.347 AC: 52822 AN: 152064 Hom.: 10822 Cov.: 33 AF XY: 0.338 AC XY: 25100 AN XY: 74338

African (AFR) AF: 0.175 AC: 7263 AN: 41504

American (AMR) AF: 0.310 AC: 4751 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1800 AN: 3466

East Asian (EAS) AF: 0.0240 AC: 124 AN: 5172

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4814

European-Finnish (FIN) AF: 0.372 AC: 3925 AN: 10564

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32462 AN: 67920

Other (OTH) AF: 0.364 AC: 769 AN: 2114

Alfa AF: 0.433 Hom.: 66831

Bravo AF: 0.331

Asia WGS AF: 0.155 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.45
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs13280813; hg19: chr8-11425105;