20-17101687-G-C

Position:

• chr20-17101687-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.710

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs852027; hg19: chr20-17082332;