rs2240747

chr19-5456919-A-C

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 0.182 in 950,814 control chromosomes in the GnomAD database, including 17,466 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 0.17 (2616 hom., cov: 32)
  • Exomes 𝑓: 0.18 (14850 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 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: 0.172 AC: 26143 AN: 151970 Hom.: 2617 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.169

GnomAD4 exome AF: 0.184 AC: 147357 AN: 798726 Hom.: 14850 AF XY: 0.185 AC XY: 73182 AN XY: 396214

Gnomad4 AFR exome AF: 0.102

Gnomad4 AMR exome AF: 0.181

Gnomad4 ASJ exome AF: 0.221

Gnomad4 EAS exome AF: 0.393

Gnomad4 SAS exome AF: 0.207

Gnomad4 FIN exome AF: 0.238

Gnomad4 NFE exome AF: 0.169

Gnomad4 OTH exome AF: 0.187

GnomAD4 genome AF: 0.172 AC: 26161 AN: 152088 Hom.: 2616 Cov.: 32 AF XY: 0.180 AC XY: 13345 AN XY: 74344

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.169

Alfa AF: 0.175 Hom.: 3187

Bravo AF: 0.168

Asia WGS AF: 0.296 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.2
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2240747; hg19: chr19-5456930; COSMIC: COSV55774076;