ENST00000423208.2:n.202+11755G>A

Variant names:

• chr6-125695434-G-A
• rs13328298
• ENST00000423208.2:n.202+11755G>A

Variant summary

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

The ENST00000423208.2(LINC02523):​n.202+11755G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,912 control chromosomes in the GnomAD database, including 17,651 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 0.47 (17651 hom., cov: 31)
• Consequence: LINC02523 ENST00000423208.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 8 publications found

Genes affected

LINC02523 (HGNC:53542): (long intergenic non-protein coding RNA 2523)

HEY2-AS1 (HGNC:55652): (HEY2 antisense RNA 1)

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 (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02523	NR_038906.1	n.202+11755G>A		intron_variant	Intron 3 of 3
HEY2-AS1	NR_183490.1	n.682+24990C>T		intron_variant	Intron 2 of 3
HEY2-AS1	NR_183491.1	n.551+24990C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02523	ENST00000423208.2	n.202+11755G>A		intron_variant	Intron 3 of 3	1
HEY2-AS1	ENST00000427852.7	n.273+24990C>T		intron_variant	Intron 3 of 5	3
HEY2-AS1	ENST00000451660.6	n.443+24990C>T		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71563 AN: 151794 Hom.: 17618 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.472 AC: 71642 AN: 151912 Hom.: 17651 Cov.: 31 AF XY: 0.470 AC XY: 34849 AN XY: 74212

African (AFR) AF: 0.598 AC: 24766 AN: 41438

American (AMR) AF: 0.422 AC: 6447 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1938 AN: 3460

East Asian (EAS) AF: 0.152 AC: 786 AN: 5178

South Asian (SAS) AF: 0.431 AC: 2073 AN: 4810

European-Finnish (FIN) AF: 0.409 AC: 4300 AN: 10524

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.437 AC: 29658 AN: 67932

Other (OTH) AF: 0.478 AC: 1008 AN: 2108

Alfa AF: 0.460 Hom.: 2021

Bravo AF: 0.478

Asia WGS AF: 0.293 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.43
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs13328298; hg19: chr6-126016580;