rs2281517

chr14-94323450-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 0.209 in 152,174 control chromosomes in the GnomAD database, including 3,617 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 0.21 (3616 hom., cov: 32)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 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: 0.209 AC: 31729 AN: 152050 Hom.: 3607 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.209 AC: 31756 AN: 152168 Hom.: 3616 Cov.: 32 AF XY: 0.211 AC XY: 15699 AN XY: 74424

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.222

Alfa AF: 0.204 Hom.: 297

Bravo AF: 0.197

Asia WGS AF: 0.344 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	8.5
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2281517; hg19: chr14-94789787;