rs287553

Variant names:

• chr13-73330093-G-A
• rs287553

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 0.388 in 152,044 control chromosomes in the GnomAD database, including 13,288 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 0.39 (13288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 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: 0.388 AC: 58958 AN: 151924 Hom.: 13251 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.388 AC: 59045 AN: 152044 Hom.: 13288 Cov.: 32 AF XY: 0.386 AC XY: 28710 AN XY: 74314

African (AFR) AF: 0.635 AC: 26325 AN: 41476

American (AMR) AF: 0.326 AC: 4985 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2068 AN: 5178

South Asian (SAS) AF: 0.281 AC: 1350 AN: 4810

European-Finnish (FIN) AF: 0.279 AC: 2950 AN: 10556

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.279 AC: 18935 AN: 67966

Other (OTH) AF: 0.370 AC: 780 AN: 2110

Alfa AF: 0.311 Hom.: 4476

Bravo AF: 0.403

Asia WGS AF: 0.329 AC: 1145 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.5
DANN	Benign	0.82
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs287553; hg19: chr13-73904230;