3-114120575-A-T

Variant names:

• chr3-114120575-A-T
• rs1486012

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 0.533 in 152,098 control chromosomes in the GnomAD database, including 21,720 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 0.53 (21720 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80998 AN: 151978 Hom.: 21709 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.533 AC: 81040 AN: 152098 Hom.: 21720 Cov.: 33 AF XY: 0.538 AC XY: 40008 AN XY: 74350

African (AFR) AF: 0.459 AC: 19067 AN: 41496

American (AMR) AF: 0.605 AC: 9250 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2518 AN: 5184

South Asian (SAS) AF: 0.544 AC: 2626 AN: 4828

European-Finnish (FIN) AF: 0.569 AC: 6012 AN: 10564

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37535 AN: 67962

Other (OTH) AF: 0.566 AC: 1193 AN: 2108

Alfa AF: 0.533 Hom.: 2711

Bravo AF: 0.533

Asia WGS AF: 0.498 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1486012; hg19: chr3-113839422;