rs2423279

chr20-7831703-T-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 0.292 in 294,204 control chromosomes in the GnomAD database, including 13,942 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 0.29 (6895 hom., cov: 33)
  • Exomes 𝑓: 0.29 (7047 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 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: 0.293 AC: 44535 AN: 152020 Hom.: 6874 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.309

GnomAD4 exome AF: 0.290 AC: 41269 AN: 142066 Hom.: 7047 AF XY: 0.303 AC XY: 23257 AN XY: 76826

Gnomad4 AFR exome AF: 0.350

Gnomad4 AMR exome AF: 0.336

Gnomad4 ASJ exome AF: 0.314

Gnomad4 EAS exome AF: 0.293

Gnomad4 SAS exome AF: 0.474

Gnomad4 FIN exome AF: 0.213

Gnomad4 NFE exome AF: 0.244

Gnomad4 OTH exome AF: 0.284

GnomAD4 genome AF: 0.293 AC: 44605 AN: 152138 Hom.: 6895 Cov.: 33 AF XY: 0.293 AC XY: 21759 AN XY: 74386

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.316

Alfa AF: 0.269 Hom.: 5912

Bravo AF: 0.302

Asia WGS AF: 0.446 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	9.7
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2423279; hg19: chr20-7812350; COSMIC: COSV68763360;