20-17101687-G-C

Variant names:

• chr20-17101687-G-C
• rs852027

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 0.735 in 152,146 control chromosomes in the GnomAD database, including 41,188 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 0.74 (41188 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.765 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: 0.735 AC: 111786 AN: 152026 Hom.: 41160 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.735 AC: 111859 AN: 152146 Hom.: 41188 Cov.: 33 AF XY: 0.736 AC XY: 54766 AN XY: 74372

African (AFR) AF: 0.712 AC: 29568 AN: 41520

American (AMR) AF: 0.717 AC: 10962 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2345 AN: 3470

East Asian (EAS) AF: 0.770 AC: 3964 AN: 5146

South Asian (SAS) AF: 0.786 AC: 3787 AN: 4820

European-Finnish (FIN) AF: 0.793 AC: 8393 AN: 10588

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.742 AC: 50462 AN: 67996

Other (OTH) AF: 0.710 AC: 1501 AN: 2114

Alfa AF: 0.747 Hom.: 5033

Bravo AF: 0.725

Asia WGS AF: 0.788 AC: 2739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.42
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs852027; hg19: chr20-17082332;