10-69692529-T-C

Variant names:

• chr10-69692529-T-C
• rs2812533
• ENST00000434931.2:n.*77T>C

Variant summary

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

The ENST00000434931.2(LINC02651):​n.*77T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,368 control chromosomes in the GnomAD database, including 56,454 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 0.86 (56420 hom., cov: 33)
  • Exomes 𝑓: 0.90 (34 hom.)
• Consequence: LINC02651 ENST00000434931.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.07
• Publications: 15 publications found

Genes affected

LINC02651 (HGNC:54136): (long intergenic non-protein coding RNA 2651)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434931.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02651	ENST00000434931.2	TSL:4	n.*77T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130830 AN: 152164 Hom.: 56364 Cov.: 33

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.876

GnomAD4 exome AF: 0.895 AC: 77 AN: 86 Hom.: 34 AF XY: 0.914 AC XY: 53 AN XY: 58

African (AFR) AF: 0.833 AC: 5 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.667 AC: 4 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.906 AC: 58 AN: 64

Other (OTH) AF: 1.00 AC: 8 AN: 8

GnomAD4 genome AF: 0.860 AC: 130946 AN: 152282 Hom.: 56420 Cov.: 33 AF XY: 0.860 AC XY: 64054 AN XY: 74480

African (AFR) AF: 0.899 AC: 37378 AN: 41560

American (AMR) AF: 0.886 AC: 13563 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3150 AN: 3470

East Asian (EAS) AF: 0.930 AC: 4811 AN: 5172

South Asian (SAS) AF: 0.878 AC: 4239 AN: 4826

European-Finnish (FIN) AF: 0.809 AC: 8584 AN: 10614

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56351 AN: 68016

Other (OTH) AF: 0.877 AC: 1852 AN: 2112

Alfa AF: 0.847 Hom.: 110950

Bravo AF: 0.868

Asia WGS AF: 0.887 AC: 3082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0040
DANN	Benign	0.63
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs2812533; hg19: chr10-71452285;