rs3020176

Variant names:

• chr8-116935146-C-A
• rs3020176

Your query was ambiguous. Multiple possible variants found:

• chr8-116935146-C-A
• chr8-116935146-C-G
• chr8-116935146-C-T

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 0.659 in 151,840 control chromosomes in the GnomAD database, including 33,210 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 0.66 (33210 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 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: 0.659 AC: 99978 AN: 151722 Hom.: 33155 Cov.: 30

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.659 AC: 100082 AN: 151840 Hom.: 33210 Cov.: 30 AF XY: 0.667 AC XY: 49490 AN XY: 74218

African (AFR) AF: 0.708 AC: 29292 AN: 41390

American (AMR) AF: 0.731 AC: 11153 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1793 AN: 3466

East Asian (EAS) AF: 0.817 AC: 4227 AN: 5176

South Asian (SAS) AF: 0.688 AC: 3313 AN: 4816

European-Finnish (FIN) AF: 0.681 AC: 7166 AN: 10520

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41113 AN: 67904

Other (OTH) AF: 0.635 AC: 1338 AN: 2108

Alfa AF: 0.606 Hom.: 14040

Bravo AF: 0.664

Asia WGS AF: 0.725 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.025
DANN	Benign	0.46
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3020176; hg19: chr8-117947385;