3-10733074-C-T

Variant names:

• chr3-10733074-C-T
• rs1682825

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 0.824 in 151,954 control chromosomes in the GnomAD database, including 51,760 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 0.82 (51760 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 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: 0.824 AC: 125095 AN: 151836 Hom.: 51710 Cov.: 31

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.824 AC: 125201 AN: 151954 Hom.: 51760 Cov.: 31 AF XY: 0.823 AC XY: 61115 AN XY: 74270

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.808

Alfa AF: 0.811 Hom.: 100697

Bravo AF: 0.822

Asia WGS AF: 0.687 AC: 2395 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	0.28
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1682825; hg19: chr3-10774759;