6-37519268-T-C

Position:

• chr6-37519268-T-C

Variant summary

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

The NR_126057.1(LINC02520):​n.357+11564T>C 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 0.606 in 152,134 control chromosomes in the GnomAD database, including 28,553 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 0.61 (28553 hom., cov: 33)
• Consequence: LINC02520 NR_126057.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

Genes affected

LINC02520 (HGNC:53511): (long intergenic non-protein coding RNA 2520)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02520	NR_126057.1	n.357+11564T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02520	ENST00000570443.2	n.357+11564T>C		intron_variant, non_coding_transcript_variant		4
LINC02520	ENST00000689244.1	n.225+2327T>C		intron_variant, non_coding_transcript_variant
LINC02520	ENST00000690655.1	n.176+2327T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92065 AN: 152016 Hom.: 28538 Cov.: 33

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.606 AC: 92118 AN: 152134 Hom.: 28553 Cov.: 33 AF XY: 0.598 AC XY: 44493 AN XY: 74368

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.617

Alfa AF: 0.652 Hom.: 72525

Bravo AF: 0.607

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1757171; hg19: chr6-37487044;