rs3812558

Variant names:

• chr9-136374683-A-G
• rs3812558

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 0.379 in 152,090 control chromosomes in the GnomAD database, including 11,311 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 0.38 (11311 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.464 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: 0.379 AC: 57523 AN: 151972 Hom.: 11292 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.379 AC: 57593 AN: 152090 Hom.: 11311 Cov.: 33 AF XY: 0.377 AC XY: 28042 AN XY: 74334

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.355

Alfa AF: 0.419 Hom.: 2150

Bravo AF: 0.375

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3812558; hg19: chr9-139269135;