rs16832889

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000240478 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000240478	ENST00000462382.1	n.315-8479A>C		intron_variant	Intron 1 of 1	3

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

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.0387

Gnomad4 ASJ AF: 0.00894

Gnomad4 EAS AF: 0.0963

Gnomad4 SAS AF: 0.00890

Gnomad4 FIN AF: 0.0355

Gnomad4 NFE AF: 0.00995

Gnomad4 OTH AF: 0.0128

Alfa AF: 0.0113 Hom.: 7

Bravo AF: 0.0151

Asia WGS AF: 0.0450 AC: 158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16832889; hg19: chr3-181851284;