rs851058

Variant names:

• chr17-43760351-G-A
• rs851058

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 0.386 in 152,042 control chromosomes in the GnomAD database, including 11,782 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 (11782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 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: 58722 AN: 151922 Hom.: 11778 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.386 AC: 58750 AN: 152042 Hom.: 11782 Cov.: 32 AF XY: 0.392 AC XY: 29125 AN XY: 74308

African (AFR) AF: 0.278 AC: 11516 AN: 41466

American (AMR) AF: 0.397 AC: 6080 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1110 AN: 3468

East Asian (EAS) AF: 0.343 AC: 1769 AN: 5164

South Asian (SAS) AF: 0.488 AC: 2356 AN: 4824

European-Finnish (FIN) AF: 0.534 AC: 5635 AN: 10548

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29079 AN: 67956

Other (OTH) AF: 0.361 AC: 763 AN: 2114

Alfa AF: 0.411 Hom.: 1698

Bravo AF: 0.366

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs851058; hg19: chr17-41837719;