rs287553

Positions:

• chr13-73330093-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.370

Alfa AF: 0.308 Hom.: 3944

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs287553; hg19: chr13-73904230;