rs787858

Variant names:

• chr1-84239798-C-A
• rs787858

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 0.543 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.285 AC: 11768 AN: 41360

American (AMR) AF: 0.514 AC: 7846 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2211 AN: 3468

East Asian (EAS) AF: 0.418 AC: 2152 AN: 5154

South Asian (SAS) AF: 0.485 AC: 2339 AN: 4818

European-Finnish (FIN) AF: 0.706 AC: 7439 AN: 10532

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46961 AN: 67928

Other (OTH) AF: 0.552 AC: 1166 AN: 2112

Alfa AF: 0.642 Hom.: 126211

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
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs787858; hg19: chr1-84705481;