rs609418

Variant names:

• chr13-36843290-A-C
• rs609418

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 0.363 in 151,488 control chromosomes in the GnomAD database, including 11,764 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 0.36 (11764 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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: 0.363 AC: 54946 AN: 151376 Hom.: 11726 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.363 AC: 55046 AN: 151488 Hom.: 11764 Cov.: 31 AF XY: 0.365 AC XY: 26992 AN XY: 74012

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.360

Alfa AF: 0.278 Hom.: 12688

Bravo AF: 0.371

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.5
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs609418; hg19: chr13-37417427;