rs2862294

Variant names:

• chr18-39950596-A-G
• rs2862294

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 0.238 in 152,038 control chromosomes in the GnomAD database, including 4,786 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 0.24 (4786 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 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: 0.238 AC: 36182 AN: 151922 Hom.: 4784 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.238 AC: 36196 AN: 152038 Hom.: 4786 Cov.: 32 AF XY: 0.238 AC XY: 17697 AN XY: 74304

African (AFR) AF: 0.124 AC: 5141 AN: 41486

American (AMR) AF: 0.248 AC: 3782 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3472

East Asian (EAS) AF: 0.126 AC: 652 AN: 5158

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4818

European-Finnish (FIN) AF: 0.271 AC: 2861 AN: 10550

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20722 AN: 67964

Other (OTH) AF: 0.265 AC: 558 AN: 2108

Alfa AF: 0.282 Hom.: 8604

Bravo AF: 0.231

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.40
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2862294; hg19: chr18-37530560;