2-46463303-G-A

Variant names:

• chr2-46463303-G-A
• rs12619696
• ENST00000432241.5:n.365-20941G>A

Variant summary

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

The ENST00000432241.5(ENSG00000284608):​n.365-20941G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,110 control chromosomes in the GnomAD database, including 3,348 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 0.15 (3348 hom., cov: 32)
• Consequence: ENSG00000284608 ENST00000432241.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 4 publications found

Genes affected

ENSG00000284608 (HGNC:):

LINC02583 (HGNC:53812): (long intergenic non-protein coding RNA 2583)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432241.5. 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
	ENSG00000284608	ENST00000432241.5	TSL:3	n.365-20941G>A		intron	N/A
	ENSG00000253515	ENST00000517716.3	TSL:5	n.113+33100G>A		intron	N/A
	LINC02583	ENST00000843637.1		n.173+34024G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22962 AN: 151992 Hom.: 3343 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0317

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.151 AC: 22986 AN: 152110 Hom.: 3348 Cov.: 32 AF XY: 0.155 AC XY: 11527 AN XY: 74360

African (AFR) AF: 0.323 AC: 13380 AN: 41440

American (AMR) AF: 0.153 AC: 2334 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3470

East Asian (EAS) AF: 0.526 AC: 2719 AN: 5172

South Asian (SAS) AF: 0.144 AC: 695 AN: 4814

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10590

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0316 AC: 2151 AN: 68004

Other (OTH) AF: 0.136 AC: 288 AN: 2114

Alfa AF: 0.135 Hom.: 475

Bravo AF: 0.166

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.69
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs12619696; hg19: chr2-46690442;