ENST00000505396.3:n.547G>C

Variant names:

• chr5-3181087-G-C
• rs372169
• ENST00000505396.3:n.547G>C

Variant summary

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

The ENST00000505396.3(LINC01377):​n.547G>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 ENST00000505396.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.836
• Publications: 5 publications found

Genes affected

LINC01377 (HGNC:50642): (long intergenic non-protein coding RNA 1377)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01377	NR_104617.1	n.504G>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01377	ENST00000505396.3	n.547G>C		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC01377	ENST00000652864.1	n.702G>C		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01377	ENST00000692105.2	n.298G>C		non_coding_transcript_exon_variant	Exon 2 of 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

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) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.714 AC: 10 AN: 14

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.771 AC: 31948 AN: 41424

American (AMR) AF: 0.346 AC: 5268 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1780 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1370 AN: 5160

South Asian (SAS) AF: 0.333 AC: 1603 AN: 4808

European-Finnish (FIN) AF: 0.364 AC: 3829 AN: 10510

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26313 AN: 67952

Other (OTH) AF: 0.476 AC: 1005 AN: 2112

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
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs372169; hg19: chr5-3181201;