rs4812405

Variant names:

• chr20-36648182-C-A
• rs4812405

Your query was ambiguous. Multiple possible variants found:

• chr20-36648182-C-A
• chr20-36648182-C-T

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 0.0467 in 152,244 control chromosomes in the GnomAD database, including 250 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 0.047 (250 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0954 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: 0.0467 AC: 7104 AN: 152126 Hom.: 249 Cov.: 31

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0660

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0467 AC: 7109 AN: 152244 Hom.: 250 Cov.: 31 AF XY: 0.0446 AC XY: 3322 AN XY: 74436

Gnomad4 AFR AF: 0.0135

Gnomad4 AMR AF: 0.0995

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.0208

Gnomad4 NFE AF: 0.0660

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0534 Hom.: 175

Bravo AF: 0.0515

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4812405; hg19: chr20-35276585;