rs16824479

chr2-183437547-G-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, non coding transcript 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: ENST00000653710.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000653710.1	n.366-55384G>A		intron_variant, non_coding_transcript_variant

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;