3-114110499-G-T

Position:

• chr3-114110499-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 0.909 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.936

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.920

Alfa AF: 0.916 Hom.: 85026

Bravo AF: 0.906

Asia WGS AF: 0.910 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4682522; hg19: chr3-113829346;