rs854462

Variant names:

• chr17-36058726-A-G
• rs854462

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 0.245 in 152,126 control chromosomes in the GnomAD database, including 6,446 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 0.24 (6446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37131 AN: 152008 Hom.: 6413 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.227

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.245 AC: 37230 AN: 152126 Hom.: 6446 Cov.: 32 AF XY: 0.246 AC XY: 18287 AN XY: 74376

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.233

Alfa AF: 0.153 Hom.: 2964

Bravo AF: 0.262

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs854462; hg19: chr17-34386090;