rs302873

chr17-58692120-C-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 0.679 in 72,160 control chromosomes in the GnomAD database, including 14,712 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 0.69 (14519 hom., cov: 9)
  • Exomes 𝑓: 0.37 (193 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 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: 0.687 AC: 48269 AN: 70270 Hom.: 14507 Cov.: 9

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.664

GnomAD4 exome AF: 0.365 AC: 693 AN: 1898 Hom.: 193 AF XY: 0.386 AC XY: 393 AN XY: 1018

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.222

Gnomad4 ASJ exome AF: 0.333

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.342

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.439

Gnomad4 OTH exome AF: 0.438

GnomAD4 genome AF: 0.687 AC: 48277 AN: 70262 Hom.: 14519 Cov.: 9 AF XY: 0.684 AC XY: 21786 AN XY: 31850

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.665

Alfa AF: 0.624 Hom.: 2759

Bravo AF: 0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.61
Dann	Benign	0.097

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs302873; hg19: chr17-56769481; COSMIC: COSV53618722;