rs13328298

chr6-125695434-G-Achr6-125695434-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038906.1(LINC02523):n.202+11755G>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 0.472 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 NR_038906.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02523	NR_038906.1	n.202+11755G>A		intron_variant, non_coding_transcript_variant
HEY2-AS1	NR_183491.1	n.551+24990C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02523	ENST00000423208.2	n.202+11755G>A		intron_variant, non_coding_transcript_variant		1
HEY2-AS1	ENST00000656901.1	n.437+24990C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.478

Alfa AF: 0.454 Hom.: 1884

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13328298; hg19: chr6-126016580;