ENST00000656637.1:n.958G>A

Variant names:

• chr4-117411099-G-A
• rs4318720
• ENST00000656637.1:n.958G>A

Variant summary

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

The ENST00000656637.1(LINC01378):​n.958G>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 0.127 in 151,834 control chromosomes in the GnomAD database, including 1,547 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 0.13 (1547 hom., cov: 32)
• Consequence: LINC01378 ENST00000656637.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 10 publications found

Genes affected

LINC01378 (HGNC:50645): (long intergenic non-protein coding RNA 1378)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01378	ENST00000656637.1	n.958G>A		non_coding_transcript_exon_variant	Exon 4 of 4
LINC01378	ENST00000667115.1	n.621G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LINC01378	ENST00000717603.1	n.1167G>A		non_coding_transcript_exon_variant	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19293 AN: 151714 Hom.: 1538 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.127 AC: 19319 AN: 151834 Hom.: 1547 Cov.: 32 AF XY: 0.132 AC XY: 9789 AN XY: 74190

African (AFR) AF: 0.119 AC: 4929 AN: 41372

American (AMR) AF: 0.213 AC: 3250 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1705 AN: 5154

South Asian (SAS) AF: 0.202 AC: 970 AN: 4806

European-Finnish (FIN) AF: 0.121 AC: 1279 AN: 10550

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.0916 AC: 6221 AN: 67940

Other (OTH) AF: 0.155 AC: 327 AN: 2114

Alfa AF: 0.112 Hom.: 3708

Bravo AF: 0.132

Asia WGS AF: 0.257 AC: 892 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.35
DANN	Benign	0.10
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4318720; hg19: chr4-118332255;