rs16828352

Variant names:

• chr3-157818394-C-T
• rs16828352
• ENST00000651134.1:n.1312-3500G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651134.1(ENSG00000242536):​n.1312-3500G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,054 control chromosomes in the GnomAD database, including 2,758 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 0.19 (2758 hom., cov: 32)
• Consequence: ENSG00000242536 ENST00000651134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

Genes affected

ENSG00000242536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 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
ENSG00000242536	ENST00000651134.1	n.1312-3500G>A		intron_variant	Intron 12 of 12

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28659 AN: 151936 Hom.: 2760 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.189 AC: 28665 AN: 152054 Hom.: 2758 Cov.: 32 AF XY: 0.193 AC XY: 14330 AN XY: 74318

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.176

Alfa AF: 0.184 Hom.: 5076

Bravo AF: 0.190

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16828352; hg19: chr3-157536183; COSMIC: COSV66118036;