chr3-106280050-T-C

Variant names:

• chr3-106280050-T-C
• rs4449354

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 0.921 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.773 AC: 32032 AN: 41442

American (AMR) AF: 0.936 AC: 14240 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3392 AN: 3470

East Asian (EAS) AF: 0.955 AC: 4934 AN: 5168

South Asian (SAS) AF: 0.962 AC: 4638 AN: 4822

European-Finnish (FIN) AF: 0.984 AC: 10410 AN: 10580

Middle Eastern (MID) AF: 0.976 AC: 283 AN: 290

European-Non Finnish (NFE) AF: 0.988 AC: 67044 AN: 67864

Other (OTH) AF: 0.930 AC: 1958 AN: 2106

Alfa AF: 0.939 Hom.: 11851

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
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs4449354; hg19: chr3-105998897;