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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.635

Alfa AF: 0.606 Hom.: 12463

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3020176; hg19: chr8-117947385;