rs2682558

Positions:

• chr19-43543164-C-T

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 0.185 in 459,756 control chromosomes in the GnomAD database, including 7,584 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 0.19 (2078 hom., cov: 27)
  • Exomes 𝑓: 0.18 (5506 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 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: 0.190 AC: 24559 AN: 129596 Hom.: 2080 Cov.: 27

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00230

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.167

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.179

GnomAD4 exome AF: 0.183 AC: 60443 AN: 330048 Hom.: 5506 Cov.: 2 AF XY: 0.183 AC XY: 32060 AN XY: 175270

Gnomad4 AFR exome AF: 0.181

Gnomad4 AMR exome AF: 0.151

Gnomad4 ASJ exome AF: 0.150

Gnomad4 EAS exome AF: 0.000442

Gnomad4 SAS exome AF: 0.160

Gnomad4 FIN exome AF: 0.199

Gnomad4 NFE exome AF: 0.206

Gnomad4 OTH exome AF: 0.184

GnomAD4 genome AF: 0.189 AC: 24571 AN: 129708 Hom.: 2078 Cov.: 27 AF XY: 0.187 AC XY: 11798 AN XY: 63040

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.00230

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.176

Alfa AF: 0.176 Hom.: 222

Bravo AF: 0.158

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.2
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2682558; hg19: chr19-44047316;