20-4834700-A-G

Variant names:

• chr20-4834700-A-G
• rs2423066

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 0.222 in 150,504 control chromosomes in the GnomAD database, including 3,925 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 0.22 (3925 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.291 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: 0.222 AC: 33397 AN: 150390 Hom.: 3929 Cov.: 26

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.222 AC: 33406 AN: 150504 Hom.: 3925 Cov.: 26 AF XY: 0.219 AC XY: 16080 AN XY: 73472

African (AFR) AF: 0.173 AC: 7080 AN: 40946

American (AMR) AF: 0.245 AC: 3701 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 926 AN: 3454

East Asian (EAS) AF: 0.0698 AC: 357 AN: 5118

South Asian (SAS) AF: 0.304 AC: 1429 AN: 4696

European-Finnish (FIN) AF: 0.177 AC: 1842 AN: 10380

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.256 AC: 17289 AN: 67556

Other (OTH) AF: 0.231 AC: 480 AN: 2076

Alfa AF: 0.245 Hom.: 18180

Bravo AF: 0.226

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.29
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs2423066; hg19: chr20-4815346;