rs173107

chr20-6785194-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.665 in 151,940 control chromosomes in the GnomAD database, including 34,383 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 0.67 (34383 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100952 AN: 151822 Hom.: 34335 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.665 AC: 101043 AN: 151940 Hom.: 34383 Cov.: 32 AF XY: 0.663 AC XY: 49200 AN XY: 74246

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.679

Alfa AF: 0.641 Hom.: 44527

Bravo AF: 0.675

Asia WGS AF: 0.486 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	19
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs173107; hg19: chr20-6765841;