rs4873166

Variant names:

• chr8-51083515-T-C
• rs4873166

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 0.437 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.581 AC: 24097 AN: 41462

American (AMR) AF: 0.435 AC: 6643 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1517 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1918 AN: 5164

South Asian (SAS) AF: 0.512 AC: 2465 AN: 4816

European-Finnish (FIN) AF: 0.320 AC: 3379 AN: 10560

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24917 AN: 67992

Other (OTH) AF: 0.448 AC: 945 AN: 2108

Alfa AF: 0.395 Hom.: 11860

Bravo AF: 0.455

Asia WGS AF: 0.497 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.40
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs4873166; hg19: chr8-51996075;