3-114110499-G-T

Variant names:

• chr3-114110499-G-T
• rs4682522

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 0.909 in 152,052 control chromosomes in the GnomAD database, including 62,900 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 0.91 (62900 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.909 AC: 138156 AN: 151934 Hom.: 62875 Cov.: 30

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.909 AC: 138235 AN: 152052 Hom.: 62900 Cov.: 30 AF XY: 0.909 AC XY: 67584 AN XY: 74320

African (AFR) AF: 0.873 AC: 36183 AN: 41424

American (AMR) AF: 0.936 AC: 14297 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3136 AN: 3470

East Asian (EAS) AF: 0.913 AC: 4710 AN: 5158

South Asian (SAS) AF: 0.909 AC: 4378 AN: 4816

European-Finnish (FIN) AF: 0.955 AC: 10111 AN: 10590

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62413 AN: 68004

Other (OTH) AF: 0.920 AC: 1945 AN: 2114

Alfa AF: 0.913 Hom.: 122047

Bravo AF: 0.906

Asia WGS AF: 0.910 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.99
DANN	Benign	0.71
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4682522; hg19: chr3-113829346;