rs1872283

Variant names:

• chr8-106798663-G-A
• rs1872283

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 0.686 in 152,158 control chromosomes in the GnomAD database, including 36,392 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 0.69 (36392 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

ACMG classification

Verdict is Benign. Variant got -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 = 0.807 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: 0.686 AC: 104305 AN: 152040 Hom.: 36353 Cov.: 33

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.686 AC: 104397 AN: 152158 Hom.: 36392 Cov.: 33 AF XY: 0.682 AC XY: 50693 AN XY: 74366

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.710

Alfa AF: 0.659 Hom.: 55731

Bravo AF: 0.698

Asia WGS AF: 0.711 AC: 2472 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	0.0030
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1872283; hg19: chr8-107810891;