20-17906057-G-C

Variant names:

• chr20-17906057-G-C
• rs6111734

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 0.362 in 151,978 control chromosomes in the GnomAD database, including 10,895 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 0.36 (10895 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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: 0.362 AC: 54970 AN: 151860 Hom.: 10895 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.362 AC: 54997 AN: 151978 Hom.: 10895 Cov.: 31 AF XY: 0.367 AC XY: 27278 AN XY: 74256

African (AFR) AF: 0.222 AC: 9197 AN: 41472

American (AMR) AF: 0.364 AC: 5563 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3468

East Asian (EAS) AF: 0.738 AC: 3807 AN: 5156

South Asian (SAS) AF: 0.432 AC: 2080 AN: 4814

European-Finnish (FIN) AF: 0.430 AC: 4531 AN: 10536

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.397 AC: 26980 AN: 67946

Other (OTH) AF: 0.394 AC: 831 AN: 2110

Alfa AF: 0.376 Hom.: 1362

Bravo AF: 0.349

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.77
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6111734; hg19: chr20-17886701;