rs4890931

Variant names:

• chr18-76757466-T-C
• rs4890931

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 0.452 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.452 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

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.436

Alfa AF: 0.398 Hom.: 6455

Bravo AF: 0.467

Asia WGS AF: 0.399 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4890931; hg19: chr18-74469422;