rs16828352

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000242536 (HGNC:58948):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651134.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000242536	ENST00000651134.1		n.1312-3500G>A		intron	N/A

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

African (AFR) AF: 0.163 AC: 6744 AN: 41498

American (AMR) AF: 0.246 AC: 3748 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3470

East Asian (EAS) AF: 0.184 AC: 948 AN: 5164

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4810

European-Finnish (FIN) AF: 0.221 AC: 2330 AN: 10560

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12826 AN: 67972

Other (OTH) AF: 0.176 AC: 371 AN: 2108

Alfa AF: 0.186 Hom.: 10442

Bravo AF: 0.190

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.90
PhyloP100		-0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16828352;

hg19: chr3-157536183;

COSMIC: COSV66118036;