3-142898296-T-G

Variant names:

• chr3-142898296-T-G
• rs4683702

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 0.259 in 152,098 control chromosomes in the GnomAD database, including 6,031 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 0.26 (6031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 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: 0.259 AC: 39381 AN: 151980 Hom.: 6030 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.259 AC: 39383 AN: 152098 Hom.: 6031 Cov.: 32 AF XY: 0.258 AC XY: 19158 AN XY: 74372

African (AFR) AF: 0.117 AC: 4868 AN: 41516

American (AMR) AF: 0.238 AC: 3641 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1138 AN: 3466

East Asian (EAS) AF: 0.0748 AC: 388 AN: 5188

South Asian (SAS) AF: 0.123 AC: 590 AN: 4816

European-Finnish (FIN) AF: 0.378 AC: 3989 AN: 10558

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23649 AN: 67946

Other (OTH) AF: 0.262 AC: 551 AN: 2106

Alfa AF: 0.305 Hom.: 25623

Bravo AF: 0.247

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs4683702; hg19: chr3-142617138;