rs2862294

Positions:

• chr18-39950596-A-G

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 0.238 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.265

Alfa AF: 0.290 Hom.: 6977

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2862294; hg19: chr18-37530560;