rs4812466

Variant names:

• chr20-40810843-G-T
• rs4812466

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 0.305 in 151,998 control chromosomes in the GnomAD database, including 7,488 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 0.31 (7488 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 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: 0.305 AC: 46356 AN: 151878 Hom.: 7486 Cov.: 33

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.305 AC: 46415 AN: 151998 Hom.: 7488 Cov.: 33 AF XY: 0.308 AC XY: 22841 AN XY: 74274

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.281

Alfa AF: 0.290 Hom.: 1062

Bravo AF: 0.313

Asia WGS AF: 0.333 AC: 1157 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	0.21
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: rs4812466; hg19: chr20-39439483;