rs854656

Variant names:

• chr17-36018624-A-C
• rs854656

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 0.387 in 152,062 control chromosomes in the GnomAD database, including 16,723 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 0.39 (16723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.387 AC: 58743 AN: 151944 Hom.: 16681 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.387 AC: 58837 AN: 152062 Hom.: 16723 Cov.: 32 AF XY: 0.389 AC XY: 28915 AN XY: 74330

African (AFR) AF: 0.803 AC: 33294 AN: 41456

American (AMR) AF: 0.310 AC: 4745 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 742 AN: 3462

East Asian (EAS) AF: 0.412 AC: 2134 AN: 5182

South Asian (SAS) AF: 0.371 AC: 1789 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2172 AN: 10582

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12911 AN: 67964

Other (OTH) AF: 0.321 AC: 679 AN: 2114

Alfa AF: 0.265 Hom.: 4161

Bravo AF: 0.407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.52
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs854656; hg19: chr17-34345661;