rs883873

Variant names:

• chr1-91914745-A-G
• rs883873

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 0.135 in 152,216 control chromosomes in the GnomAD database, including 2,228 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 0.13 (2228 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.912
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 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: 0.135 AC: 20504 AN: 152098 Hom.: 2226 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0878

Gnomad FIN AF: 0.0343

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.135 AC: 20533 AN: 152216 Hom.: 2228 Cov.: 33 AF XY: 0.131 AC XY: 9780 AN XY: 74430

African (AFR) AF: 0.299 AC: 12398 AN: 41490

American (AMR) AF: 0.0906 AC: 1383 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0838 AC: 291 AN: 3472

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5190

South Asian (SAS) AF: 0.0871 AC: 420 AN: 4824

European-Finnish (FIN) AF: 0.0343 AC: 364 AN: 10620

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0782 AC: 5323 AN: 68026

Other (OTH) AF: 0.125 AC: 265 AN: 2116

Alfa AF: 0.0940 Hom.: 736

Bravo AF: 0.145

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs883873; hg19: chr1-92380302;