3-14776147-G-A

Variant names:

• chr3-14776147-G-A
• rs853334

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 0.547 in 152,088 control chromosomes in the GnomAD database, including 23,899 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 0.55 (23899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 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: 0.547 AC: 83140 AN: 151970 Hom.: 23892 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.547 AC: 83173 AN: 152088 Hom.: 23899 Cov.: 32 AF XY: 0.550 AC XY: 40881 AN XY: 74374

African (AFR) AF: 0.365 AC: 15125 AN: 41462

American (AMR) AF: 0.540 AC: 8248 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2186 AN: 3466

East Asian (EAS) AF: 0.483 AC: 2496 AN: 5164

South Asian (SAS) AF: 0.523 AC: 2524 AN: 4824

European-Finnish (FIN) AF: 0.706 AC: 7472 AN: 10578

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43232 AN: 67998

Other (OTH) AF: 0.557 AC: 1175 AN: 2110

Alfa AF: 0.596 Hom.: 40722

Bravo AF: 0.527

Asia WGS AF: 0.482 AC: 1679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.86
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs853334; hg19: chr3-14817654;