rs16824479

Variant names:

• chr2-183437547-G-A
• rs16824479
• ENST00000653710.1:n.366-55384G>A

Variant summary

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

The ENST00000653710.1(ENSG00000287621):​n.366-55384G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0377 in 152,284 control chromosomes in the GnomAD database, including 393 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 0.038 (393 hom., cov: 32)
• Consequence: ENSG00000287621 ENST00000653710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

Genes affected

ENSG00000287621 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 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
ENSG00000287621	ENST00000653710.1	n.366-55384G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0376 AC: 5716 AN: 152166 Hom.: 389 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0381

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.0449

Gnomad FIN AF: 0.0688

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0377 AC: 5735 AN: 152284 Hom.: 393 Cov.: 32 AF XY: 0.0421 AC XY: 3132 AN XY: 74460

Gnomad4 AFR AF: 0.0203

Gnomad4 AMR AF: 0.0382

Gnomad4 ASJ AF: 0.0642

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.0455

Gnomad4 FIN AF: 0.0688

Gnomad4 NFE AF: 0.0191

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.0252 Hom.: 8

Bravo AF: 0.0372

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16824479; hg19: chr2-184302275;