rs4750316

chr10-6351298-C-Gchr10-6351298-C-T

Variant summary

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

The NR_148966.1(LINC02656):n.983C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 156,658 control chromosomes in the GnomAD database, including 46,651 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 0.77 (45083 hom., cov: 30)
  • Exomes 𝑓: 0.81 (1568 hom.)
• Consequence: LINC02656 NR_148966.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163

Genes affected

LINC02656 (HGNC:54142): (long intergenic non-protein coding RNA 2656)

LINC02649 (HGNC:54134): (long intergenic non-protein coding RNA 2649)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02656	NR_148966.1	n.983C>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02656	ENST00000391437.2	n.983C>G		non_coding_transcript_exon_variant	1/1
LINC02649	ENST00000659311.1	n.623-1609C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116242 AN: 151808 Hom.: 45066 Cov.: 30

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.782

GnomAD4 exome AF: 0.812 AC: 3843 AN: 4734 Hom.: 1568 Cov.: 0 AF XY: 0.803 AC XY: 1990 AN XY: 2478

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.836

Gnomad4 ASJ exome AF: 0.844

Gnomad4 EAS exome AF: 0.878

Gnomad4 SAS exome AF: 0.814

Gnomad4 FIN exome AF: 0.921

Gnomad4 NFE exome AF: 0.799

Gnomad4 OTH exome AF: 0.865

GnomAD4 genome AF: 0.766 AC: 116307 AN: 151924 Hom.: 45083 Cov.: 30 AF XY: 0.769 AC XY: 57094 AN XY: 74234

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.779

Alfa AF: 0.805 Hom.: 27079

Bravo AF: 0.762

Asia WGS AF: 0.837 AC: 2913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.5
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4750316; hg19: chr10-6393260;