3-114120575-A-T

Variant names:

• chr3-114120575-A-T
• rs1486012

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 0.533 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.533 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

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.566

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1486012; hg19: chr3-113839422;