rs2874116

Variant names:

• chr18-58792367-G-A
• rs2874116

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.359 in 151,956 control chromosomes in the GnomAD database, including 10,809 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 (10809 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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: 0.359 AC: 54528 AN: 151840 Hom.: 10806 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.359 AC: 54548 AN: 151956 Hom.: 10809 Cov.: 31 AF XY: 0.352 AC XY: 26165 AN XY: 74236

African (AFR) AF: 0.201 AC: 8315 AN: 41422

American (AMR) AF: 0.422 AC: 6441 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1803 AN: 3472

East Asian (EAS) AF: 0.229 AC: 1186 AN: 5172

South Asian (SAS) AF: 0.254 AC: 1220 AN: 4812

European-Finnish (FIN) AF: 0.327 AC: 3459 AN: 10562

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30810 AN: 67954

Other (OTH) AF: 0.398 AC: 841 AN: 2114

Alfa AF: 0.390 Hom.: 4320

Bravo AF: 0.363

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.65
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2874116; hg19: chr18-56459599;