rs4873166

Variant names:

• chr8-51083515-T-C
• rs4873166

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 0.437 in 152,034 control chromosomes in the GnomAD database, including 15,278 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 0.44 (15278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 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: 0.437 AC: 66326 AN: 151916 Hom.: 15236 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.437 AC: 66430 AN: 152034 Hom.: 15278 Cov.: 32 AF XY: 0.436 AC XY: 32363 AN XY: 74304

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.448

Alfa AF: 0.394 Hom.: 9646

Bravo AF: 0.455

Asia WGS AF: 0.497 AC: 1730 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	1.0
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4873166; hg19: chr8-51996075;