chr6-125701456-G-T

Position:

• chr6-125701456-G-T

Variant summary

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

The NR_038906.1(LINC02523):​n.203-16002G>T 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 0.395 in 152,056 control chromosomes in the GnomAD database, including 12,152 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 0.40 (12152 hom., cov: 32)
• Consequence: LINC02523 NR_038906.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02523	NR_038906.1	n.203-16002G>T		intron_variant, non_coding_transcript_variant
HEY2-AS1	NR_183491.1	n.551+18968C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02523	ENST00000423208.2	n.203-16002G>T		intron_variant, non_coding_transcript_variant		1
HEY2-AS1	ENST00000656901.1	n.437+18968C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60042 AN: 151938 Hom.: 12145 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.395 AC: 60073 AN: 152056 Hom.: 12152 Cov.: 32 AF XY: 0.395 AC XY: 29337 AN XY: 74320

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.412

Alfa AF: 0.405 Hom.: 18220

Bravo AF: 0.396

Asia WGS AF: 0.252 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1777220; hg19: chr6-126022602;