3-106280050-T-C

Variant names:

• chr3-106280050-T-C
• rs4449354

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 0.921 in 151,874 control chromosomes in the GnomAD database, including 65,035 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 0.92 (65035 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 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: 0.921 AC: 139793 AN: 151754 Hom.: 65030 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.974

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.921 AC: 139843 AN: 151874 Hom.: 65035 Cov.: 31 AF XY: 0.922 AC XY: 68419 AN XY: 74230

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.984

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.930

Alfa AF: 0.944 Hom.: 11621

Bravo AF: 0.912

Asia WGS AF: 0.939 AC: 3225 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.82
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4449354; hg19: chr3-105998897;