rs16832889

Variant names:

• chr3-182133496-A-C
• rs16832889
• ENST00000462382.1:n.315-8479A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000462382.1(ENSG00000240478):​n.315-8479A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0152 in 152,376 control chromosomes in the GnomAD database, including 50 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 0.015 (50 hom., cov: 32)
• Consequence: ENSG00000240478 ENST00000462382.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693
• Publications: 2 publications found

Genes affected

ENSG00000240478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0893 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000462382.1. 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
	ENSG00000240478	ENST00000462382.1	TSL:3	n.315-8479A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0152 AC: 2313 AN: 152256 Hom.: 50 Cov.: 32

Gnomad AFR AF: 0.00166

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.00894

Gnomad EAS AF: 0.0960

Gnomad SAS AF: 0.00889

Gnomad FIN AF: 0.0355

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00993

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0152 AC: 2316 AN: 152376 Hom.: 50 Cov.: 32 AF XY: 0.0172 AC XY: 1284 AN XY: 74518

African (AFR) AF: 0.00166 AC: 69 AN: 41594

American (AMR) AF: 0.0387 AC: 593 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00894 AC: 31 AN: 3468

East Asian (EAS) AF: 0.0963 AC: 499 AN: 5180

South Asian (SAS) AF: 0.00890 AC: 43 AN: 4832

European-Finnish (FIN) AF: 0.0355 AC: 377 AN: 10630

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00995 AC: 677 AN: 68042

Other (OTH) AF: 0.0128 AC: 27 AN: 2114

Alfa AF: 0.0119 Hom.: 34

Bravo AF: 0.0151

Asia WGS AF: 0.0450 AC: 158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.23
DANN	Benign	0.40
PhyloP100		-0.69

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: rs16832889;

hg19: chr3-181851284;