rs9866505

Variant names:

• chr3-193958323-C-T
• rs9866505
• ENST00000397645.2:n.664G>A

Variant summary

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

The ENST00000397645.2(LINC02026):​n.664G>A 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 0.383 in 151,992 control chromosomes in the GnomAD database, including 11,467 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 0.38 (11466 hom., cov: 32)
  • Exomes 𝑓: 0.44 (1 hom.)
• Consequence: LINC02026 ENST00000397645.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 2 publications found

Genes affected

LINC02026 (HGNC:52861): (long intergenic non-protein coding RNA 2026)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02026	NR_033944.1	n.664G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02026	ENST00000397645.2	n.664G>A		non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC02026	ENST00000736877.1	n.166G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02026	ENST00000736878.1	n.395G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58187 AN: 151856 Hom.: 11447 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.360

GnomAD4 exome AF: 0.444 AC: 8 AN: 18 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 6 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.429 AC: 6 AN: 14

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.383 AC: 58257 AN: 151974 Hom.: 11466 Cov.: 32 AF XY: 0.380 AC XY: 28209 AN XY: 74262

African (AFR) AF: 0.483 AC: 20029 AN: 41430

American (AMR) AF: 0.338 AC: 5162 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3468

East Asian (EAS) AF: 0.282 AC: 1452 AN: 5150

South Asian (SAS) AF: 0.292 AC: 1404 AN: 4816

European-Finnish (FIN) AF: 0.384 AC: 4050 AN: 10550

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24090 AN: 67964

Other (OTH) AF: 0.365 AC: 768 AN: 2106

Alfa AF: 0.371 Hom.: 4487

Bravo AF: 0.386

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.84
DANN	Benign	0.74
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs9866505; hg19: chr3-193676112;