rs4890931

Variant names:

• chr18-76757466-T-C
• rs4890931

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 0.452 in 152,182 control chromosomes in the GnomAD database, including 17,544 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 0.45 (17544 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68690 AN: 152064 Hom.: 17514 Cov.: 33

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.452 AC: 68774 AN: 152182 Hom.: 17544 Cov.: 33 AF XY: 0.449 AC XY: 33429 AN XY: 74400

African (AFR) AF: 0.696 AC: 28882 AN: 41516

American (AMR) AF: 0.370 AC: 5649 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1609 AN: 5178

South Asian (SAS) AF: 0.493 AC: 2380 AN: 4830

European-Finnish (FIN) AF: 0.304 AC: 3223 AN: 10602

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24051 AN: 67994

Other (OTH) AF: 0.436 AC: 921 AN: 2112

Alfa AF: 0.398 Hom.: 7163

Bravo AF: 0.467

Asia WGS AF: 0.399 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.63
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs4890931; hg19: chr18-74469422;