rs853334

Variant names:

• chr3-14776147-G-A
• rs853334

Your query was ambiguous. Multiple possible variants found:

• chr3-14776147-G-A
• chr3-14776147-G-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 0.547 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.547 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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.557

Alfa AF: 0.608 Hom.: 28914

Bravo AF: 0.527

Asia WGS AF: 0.482 AC: 1679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs853334; hg19: chr3-14817654;