rs1077767

Positions:

• chr4-184512851-T-C

Variant summary

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

The NR_147158.1(LINC02427):​n.83-3526A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,088 control chromosomes in the GnomAD database, including 14,322 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 0.42 (14322 hom., cov: 32)
• Consequence: LINC02427 NR_147158.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

LINC02427 (HGNC:53358): (long intergenic non-protein coding RNA 2427)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02427	NR_147158.1	n.83-3526A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02427	ENST00000605270.6	n.126-3526A>G		intron_variant, non_coding_transcript_variant		2
LINC02427	ENST00000696856.1	n.377A>G		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64096 AN: 151970 Hom.: 14287 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.407

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.422 AC: 64176 AN: 152088 Hom.: 14322 Cov.: 32 AF XY: 0.430 AC XY: 31959 AN XY: 74356

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.414

Alfa AF: 0.368 Hom.: 14310

Bravo AF: 0.417

Asia WGS AF: 0.613 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.23
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1077767; hg19: chr4-185434005;