rs211840

Variant names:

• chr20-39846239-T-G
• rs211840

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 0.432 in 152,008 control chromosomes in the GnomAD database, including 15,452 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 0.43 (15452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 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: 0.432 AC: 65613 AN: 151890 Hom.: 15424 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.432 AC: 65696 AN: 152008 Hom.: 15452 Cov.: 32 AF XY: 0.430 AC XY: 31940 AN XY: 74280

African (AFR) AF: 0.635 AC: 26295 AN: 41438

American (AMR) AF: 0.371 AC: 5675 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1004 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1781 AN: 5172

South Asian (SAS) AF: 0.324 AC: 1562 AN: 4814

European-Finnish (FIN) AF: 0.416 AC: 4393 AN: 10548

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23815 AN: 67962

Other (OTH) AF: 0.362 AC: 764 AN: 2112

Alfa AF: 0.366 Hom.: 13175

Bravo AF: 0.439

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs211840; hg19: chr20-38474881;