chr2-183437547-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000287621 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000287621	ENST00000804704.1	n.210-87521G>A		intron_variant	Intron 2 of 2
ENSG00000287621	ENST00000804705.1	n.282-87521G>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

African (AFR) AF: 0.0203 AC: 844 AN: 41566

American (AMR) AF: 0.0382 AC: 584 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0642 AC: 223 AN: 3472

East Asian (EAS) AF: 0.337 AC: 1746 AN: 5180

South Asian (SAS) AF: 0.0455 AC: 220 AN: 4830

European-Finnish (FIN) AF: 0.0688 AC: 730 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0191 AC: 1296 AN: 68022

Other (OTH) AF: 0.0417 AC: 88 AN: 2112

Alfa AF: 0.0257 Hom.: 10

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
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs16824479; hg19: chr2-184302275;