rs173107

Variant names:

• chr20-6785194-A-C
• rs173107

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.784 AC: 32473 AN: 41446

American (AMR) AF: 0.649 AC: 9907 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2429 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1675 AN: 5162

South Asian (SAS) AF: 0.605 AC: 2916 AN: 4816

European-Finnish (FIN) AF: 0.624 AC: 6570 AN: 10536

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.629 AC: 42747 AN: 67936

Other (OTH) AF: 0.679 AC: 1425 AN: 2100

Alfa AF: 0.643 Hom.: 67556

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs173107; hg19: chr20-6765841;