rs7547921

Positions:

• chr1-38136401-C-A

Variant summary

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

The ENST00000641212.1(LINC02786):​n.121G>T 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 0.107 in 152,262 control chromosomes in the GnomAD database, including 949 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 0.11 (949 hom., cov: 32)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: LINC02786 ENST00000641212.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

LINC02786 (HGNC:54307): (long intergenic non-protein coding RNA 2786)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02786	XR_001737991.3	n.132G>T		non_coding_transcript_exon_variant	2/6
LINC02786	XR_007065917.1	n.132G>T		non_coding_transcript_exon_variant	2/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02786	ENST00000641212.1	n.121G>T		non_coding_transcript_exon_variant	2/5

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16316 AN: 152102 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0774

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.119 AC: 5 AN: 42 Hom.: 0 Cov.: 0 AF XY: 0.0714 AC XY: 2 AN XY: 28

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.0625

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.107 AC: 16325 AN: 152220 Hom.: 949 Cov.: 32 AF XY: 0.109 AC XY: 8094 AN XY: 74424

Gnomad4 AFR AF: 0.0895

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.0781

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.110

Alfa AF: 0.104 Hom.: 849

Bravo AF: 0.114

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	18
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7547921; hg19: chr1-38602073;