rs359965

chr2-218976169-G-A

Variant summary

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

The ENST00000419101.3(LINC00608):n.540G>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 0.0538 in 152,242 control chromosomes in the GnomAD database, including 406 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 0.054 (406 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC00608 ENST00000419101.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

Genes affected

LINC00608 (HGNC:27179): (long intergenic non-protein coding RNA 608)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00608	ENST00000419101.3	n.540G>A		non_coding_transcript_exon_variant	2/3	5
LINC00608	ENST00000600415.1	n.151+420G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0537 AC: 8175 AN: 152124 Hom.: 408 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0309

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0275

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.0454

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0538 AC: 8189 AN: 152242 Hom.: 406 Cov.: 32 AF XY: 0.0568 AC XY: 4226 AN XY: 74440

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.0275

Gnomad4 NFE AF: 0.0114

Gnomad4 OTH AF: 0.0482

Alfa AF: 0.0228 Hom.: 243

Bravo AF: 0.0551

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.9
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs359965; hg19: chr2-219840891;