3-106158618-C-T

Variant names:

• chr3-106158618-C-T
• rs6809315

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 0.712 in 152,112 control chromosomes in the GnomAD database, including 38,829 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 0.71 (38829 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 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: 0.712 AC: 108214 AN: 151994 Hom.: 38805 Cov.: 33

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.712 AC: 108293 AN: 152112 Hom.: 38829 Cov.: 33 AF XY: 0.714 AC XY: 53109 AN XY: 74372

African (AFR) AF: 0.729 AC: 30253 AN: 41488

American (AMR) AF: 0.752 AC: 11493 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2563 AN: 3472

East Asian (EAS) AF: 0.813 AC: 4206 AN: 5174

South Asian (SAS) AF: 0.548 AC: 2649 AN: 4830

European-Finnish (FIN) AF: 0.801 AC: 8474 AN: 10578

Middle Eastern (MID) AF: 0.734 AC: 213 AN: 290

European-Non Finnish (NFE) AF: 0.683 AC: 46418 AN: 67982

Other (OTH) AF: 0.721 AC: 1523 AN: 2112

Alfa AF: 0.687 Hom.: 24631

Bravo AF: 0.714

Asia WGS AF: 0.671 AC: 2333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.21
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6809315; hg19: chr3-105877465;