chr3-114116084-C-G

Variant names:

• chr3-114116084-C-G
• rs2046496

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 0.401 in 152,086 control chromosomes in the GnomAD database, including 13,920 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 0.40 (13920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60984 AN: 151968 Hom.: 13919 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.401 AC: 60984 AN: 152086 Hom.: 13920 Cov.: 32 AF XY: 0.408 AC XY: 30304 AN XY: 74334

African (AFR) AF: 0.158 AC: 6570 AN: 41510

American (AMR) AF: 0.529 AC: 8087 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1880 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2177 AN: 5166

South Asian (SAS) AF: 0.476 AC: 2298 AN: 4828

European-Finnish (FIN) AF: 0.544 AC: 5737 AN: 10552

Middle Eastern (MID) AF: 0.531 AC: 154 AN: 290

European-Non Finnish (NFE) AF: 0.482 AC: 32735 AN: 67960

Other (OTH) AF: 0.452 AC: 956 AN: 2116

Alfa AF: 0.301 Hom.: 846

Bravo AF: 0.388

Asia WGS AF: 0.416 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.27
DANN	Benign	0.72
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2046496; hg19: chr3-113834931;