rs854462

Variant names:

• chr17-36058726-A-G
• rs854462

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.485 AC: 20098 AN: 41444

American (AMR) AF: 0.265 AC: 4047 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.111 AC: 576 AN: 5176

South Asian (SAS) AF: 0.216 AC: 1044 AN: 4824

European-Finnish (FIN) AF: 0.155 AC: 1644 AN: 10600

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8743 AN: 68008

Other (OTH) AF: 0.233 AC: 491 AN: 2108

Alfa AF: 0.165 Hom.: 4608

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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs854462; hg19: chr17-34386090;