ENST00000391437.2:n.983C>G

Variant names:

• chr10-6351298-C-G
• rs4750316
• ENST00000391437.2:n.983C>G

Variant summary

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

The ENST00000391437.2(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 ENST00000391437.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 65 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02656	NR_148966.1	n.983C>G		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02656	ENST00000391437.2	n.983C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02649	ENST00000659311.1	n.623-1609C>G		intron_variant	Intron 4 of 4
LINC02649	ENST00000783921.1	n.405+6518C>G		intron_variant	Intron 5 of 5

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

African (AFR) AF: 0.750 AC: 12 AN: 16

American (AMR) AF: 0.836 AC: 624 AN: 746

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 27 AN: 32

East Asian (EAS) AF: 0.878 AC: 86 AN: 98

South Asian (SAS) AF: 0.814 AC: 324 AN: 398

European-Finnish (FIN) AF: 0.921 AC: 35 AN: 38

Middle Eastern (MID) AF: 0.750 AC: 9 AN: 12

European-Non Finnish (NFE) AF: 0.799 AC: 2546 AN: 3186

Other (OTH) AF: 0.865 AC: 180 AN: 208

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

African (AFR) AF: 0.620 AC: 25677 AN: 41398

American (AMR) AF: 0.846 AC: 12911 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2838 AN: 3468

East Asian (EAS) AF: 0.883 AC: 4559 AN: 5164

South Asian (SAS) AF: 0.817 AC: 3928 AN: 4810

European-Finnish (FIN) AF: 0.817 AC: 8596 AN: 10526

Middle Eastern (MID) AF: 0.797 AC: 231 AN: 290

European-Non Finnish (NFE) AF: 0.812 AC: 55169 AN: 67982

Other (OTH) AF: 0.779 AC: 1645 AN: 2112

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
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4750316; hg19: chr10-6393260;