rs1077767

Variant names:

• chr4-184512851-T-C
• rs1077767
• ENST00000696856.1:n.377A>G

Variant summary

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

The ENST00000696856.1(LINC02427):​n.377A>G 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 0.422 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 ENST00000696856.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02427	NR_147158.1	n.83-3526A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02427	ENST00000696856.1	n.377A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LINC02427	ENST00000772711.1	n.177A>G		non_coding_transcript_exon_variant	Exon 2 of 4
LINC02427	ENST00000772712.1	n.179A>G		non_coding_transcript_exon_variant	Exon 2 of 3
LINC02427	ENST00000605270.7	n.131-3526A>G		intron_variant	Intron 1 of 2	2

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

African (AFR) AF: 0.515 AC: 21375 AN: 41466

American (AMR) AF: 0.402 AC: 6150 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3377 AN: 5162

South Asian (SAS) AF: 0.512 AC: 2467 AN: 4822

European-Finnish (FIN) AF: 0.420 AC: 4441 AN: 10576

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24096 AN: 67984

Other (OTH) AF: 0.414 AC: 874 AN: 2112

Alfa AF: 0.379 Hom.: 36337

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1077767; hg19: chr4-185434005;