rs4812412

Variant names:

• chr20-39839032-A-G
• rs4812412

Your query was ambiguous. Multiple possible variants found:

• chr20-39839032-A-G
• chr20-39839032-A-T

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 0.468 in 152,042 control chromosomes in the GnomAD database, including 17,458 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 0.47 (17458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.527 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: 0.468 AC: 71151 AN: 151924 Hom.: 17447 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.468 AC: 71192 AN: 152042 Hom.: 17458 Cov.: 32 AF XY: 0.470 AC XY: 34940 AN XY: 74310

African (AFR) AF: 0.312 AC: 12934 AN: 41466

American (AMR) AF: 0.531 AC: 8109 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1994 AN: 3466

East Asian (EAS) AF: 0.527 AC: 2727 AN: 5176

South Asian (SAS) AF: 0.542 AC: 2608 AN: 4816

European-Finnish (FIN) AF: 0.462 AC: 4882 AN: 10560

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36106 AN: 67976

Other (OTH) AF: 0.524 AC: 1107 AN: 2112

Alfa AF: 0.504 Hom.: 11332

Bravo AF: 0.467

Asia WGS AF: 0.528 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.50
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs4812412; hg19: chr20-38467674;