rs886929

Variant names:

• chr17-57723282-G-A
• rs886929

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 0.314 in 152,052 control chromosomes in the GnomAD database, including 8,072 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 0.31 (8072 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 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: 0.314 AC: 47719 AN: 151934 Hom.: 8069 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.314 AC: 47749 AN: 152052 Hom.: 8072 Cov.: 32 AF XY: 0.309 AC XY: 22977 AN XY: 74320

African (AFR) AF: 0.439 AC: 18189 AN: 41452

American (AMR) AF: 0.236 AC: 3608 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 910 AN: 3470

East Asian (EAS) AF: 0.182 AC: 941 AN: 5172

South Asian (SAS) AF: 0.300 AC: 1445 AN: 4816

European-Finnish (FIN) AF: 0.222 AC: 2350 AN: 10582

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19294 AN: 67958

Other (OTH) AF: 0.311 AC: 658 AN: 2114

Alfa AF: 0.297 Hom.: 4191

Bravo AF: 0.319

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs886929; hg19: chr17-55800643;