rs13089920

Variant names:

• chr3-78503082-A-G
• rs13089920

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 0.278 in 152,136 control chromosomes in the GnomAD database, including 6,701 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 0.28 (6701 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

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 = 0.425 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: 0.278 AC: 42227 AN: 152018 Hom.: 6680 Cov.: 33

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.278 AC: 42283 AN: 152136 Hom.: 6701 Cov.: 33 AF XY: 0.273 AC XY: 20301 AN XY: 74376

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0483

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.274

Alfa AF: 0.241 Hom.: 4488

Bravo AF: 0.292

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.8
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13089920; hg19: chr3-78552232;