2-183489082-G-A

Variant names:

• chr2-183489082-G-A
• rs13409979
• ENST00000653710.1:n.366-3849G>A

Variant summary

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

The ENST00000653710.1(ENSG00000287621):​n.366-3849G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,894 control chromosomes in the GnomAD database, including 1,533 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 0.14 (1533 hom., cov: 32)
• Consequence: ENSG00000287621 ENST00000653710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653710.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287621	ENST00000653710.1		n.366-3849G>A		intron	N/A
	ENSG00000287621	ENST00000804704.1		n.210-35986G>A		intron	N/A
	ENSG00000287621	ENST00000804705.1		n.282-35986G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20714 AN: 151776 Hom.: 1535 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0727

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.136 AC: 20714 AN: 151894 Hom.: 1533 Cov.: 32 AF XY: 0.134 AC XY: 9985 AN XY: 74244

African (AFR) AF: 0.179 AC: 7389 AN: 41380

American (AMR) AF: 0.132 AC: 2020 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3468

East Asian (EAS) AF: 0.0613 AC: 317 AN: 5172

South Asian (SAS) AF: 0.219 AC: 1055 AN: 4810

European-Finnish (FIN) AF: 0.0542 AC: 572 AN: 10552

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.125 AC: 8514 AN: 67948

Other (OTH) AF: 0.143 AC: 302 AN: 2106

Alfa AF: 0.127 Hom.: 4461

Bravo AF: 0.141

Asia WGS AF: 0.143 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.71
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs13409979; hg19: chr2-184353810;