rs787858

Variant names:

• chr1-84239798-C-A
• rs787858

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 0.543 in 151,834 control chromosomes in the GnomAD database, including 24,856 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 0.54 (24856 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.686 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: 0.543 AC: 82444 AN: 151718 Hom.: 24854 Cov.: 30

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.543 AC: 82448 AN: 151834 Hom.: 24856 Cov.: 30 AF XY: 0.542 AC XY: 40240 AN XY: 74226

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.552

Alfa AF: 0.661 Hom.: 64532

Bravo AF: 0.519

Asia WGS AF: 0.440 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs787858; hg19: chr1-84705481;