rs13155209

Variant names:

• chr5-10788807-G-T
• rs13155209

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 0.469 in 152,112 control chromosomes in the GnomAD database, including 20,522 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 0.47 (20522 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 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: 0.469 AC: 71305 AN: 151994 Hom.: 20526 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.469 AC: 71294 AN: 152112 Hom.: 20522 Cov.: 33 AF XY: 0.462 AC XY: 34335 AN XY: 74364

African (AFR) AF: 0.179 AC: 7413 AN: 41506

American (AMR) AF: 0.481 AC: 7343 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2146 AN: 3472

East Asian (EAS) AF: 0.00579 AC: 30 AN: 5180

South Asian (SAS) AF: 0.327 AC: 1573 AN: 4812

European-Finnish (FIN) AF: 0.625 AC: 6605 AN: 10562

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44596 AN: 67984

Other (OTH) AF: 0.463 AC: 980 AN: 2116

Alfa AF: 0.589 Hom.: 47373

Bravo AF: 0.445

Asia WGS AF: 0.150 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.45
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs13155209; hg19: chr5-10788919;