chr5-3181087-G-C

Position:

• chr5-3181087-G-C

Variant summary

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

The NR_104617.1(LINC01377):​n.504G>C 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 0.484 in 151,904 control chromosomes in the GnomAD database, including 20,290 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 0.48 (20287 hom., cov: 32)
  • Exomes 𝑓: 0.61 (3 hom.)
• Consequence: LINC01377 NR_104617.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836

Genes affected

LINC01377 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01377	NR_104617.1	n.504G>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01377	ENST00000652864.1	n.702G>C		non_coding_transcript_exon_variant	3/3
LINC01377	ENST00000505396.2	n.504G>C		non_coding_transcript_exon_variant	2/2	2
LINC01377	ENST00000692105.1	n.268G>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73442 AN: 151766 Hom.: 20249 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.474

GnomAD4 exome AF: 0.611 AC: 11 AN: 18 Hom.: 3 Cov.: 0 AF XY: 0.643 AC XY: 9 AN XY: 14

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.714

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.484 AC: 73538 AN: 151886 Hom.: 20287 Cov.: 32 AF XY: 0.477 AC XY: 35423 AN XY: 74200

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.476

Alfa AF: 0.250 Hom.: 517

Bravo AF: 0.499

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs372169; hg19: chr5-3181201;