chr3-114127166-T-A

Variant names:

• chr3-114127166-T-A
• rs2399496

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 0.459 in 152,044 control chromosomes in the GnomAD database, including 16,492 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 0.46 (16492 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 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: 0.459 AC: 69783 AN: 151926 Hom.: 16484 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.459 AC: 69806 AN: 152044 Hom.: 16492 Cov.: 33 AF XY: 0.461 AC XY: 34253 AN XY: 74302

African (AFR) AF: 0.340 AC: 14105 AN: 41476

American (AMR) AF: 0.532 AC: 8135 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2079 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2840 AN: 5184

South Asian (SAS) AF: 0.506 AC: 2444 AN: 4826

European-Finnish (FIN) AF: 0.451 AC: 4743 AN: 10528

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33772 AN: 67964

Other (OTH) AF: 0.496 AC: 1049 AN: 2114

Alfa AF: 0.463 Hom.: 2085

Bravo AF: 0.458

Asia WGS AF: 0.484 AC: 1678 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.36
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2399496; hg19: chr3-113846013;