rs1818116

Variant names:

• chr5-32841828-A-G
• rs1818116

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 0.376 in 152,074 control chromosomes in the GnomAD database, including 10,869 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 (10869 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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: 0.376 AC: 57090 AN: 151956 Hom.: 10874 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.376 AC: 57113 AN: 152074 Hom.: 10869 Cov.: 32 AF XY: 0.372 AC XY: 27665 AN XY: 74332

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.414

Alfa AF: 0.391 Hom.: 15773

Bravo AF: 0.373

Asia WGS AF: 0.365 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1818116; hg19: chr5-32841934;