rs1537788

Variant names:

• chr13-20290433-C-T
• rs1537788

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 0.392 in 151,958 control chromosomes in the GnomAD database, including 12,009 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 (12009 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.392 AC: 59561 AN: 151840 Hom.: 12006 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.392 AC: 59584 AN: 151958 Hom.: 12009 Cov.: 32 AF XY: 0.391 AC XY: 29031 AN XY: 74278

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.388

Alfa AF: 0.362 Hom.: 4736

Bravo AF: 0.409

Asia WGS AF: 0.353 AC: 1228 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.096
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1537788; hg19: chr13-20864572;