1-87148400-T-C

Variant names:

• chr1-87148400-T-C
• rs4529687
• ENST00000370548.3:c.871+14682T>C

Variant summary

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

The ENST00000370548.3(ENSG00000267561):​c.871+14682T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,738 control chromosomes in the GnomAD database, including 28,970 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 0.61 (28970 hom., cov: 30)
• Consequence: ENSG00000267561 ENST00000370548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 3 publications found

Genes affected

ENSG00000267561 (HGNC:):

LINC01140 (HGNC:27922): (long intergenic non-protein coding RNA 1140)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01140	NR_026989.1	n.335+14682T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267561	ENST00000370548.3	c.871+14682T>C		intron_variant	Intron 7 of 7	2		ENSP00000359579.1
LINC01140	ENST00000469312.6	n.335+14682T>C		intron_variant	Intron 2 of 3	5
LINC01140	ENST00000490006.6	n.326+14682T>C		intron_variant	Intron 2 of 2	2
LINC01140	ENST00000587165.1	n.311-13622T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93263 AN: 151620 Hom.: 28958 Cov.: 30

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.615 AC: 93316 AN: 151738 Hom.: 28970 Cov.: 30 AF XY: 0.615 AC XY: 45614 AN XY: 74172

African (AFR) AF: 0.601 AC: 24821 AN: 41316

American (AMR) AF: 0.683 AC: 10427 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2094 AN: 3468

East Asian (EAS) AF: 0.841 AC: 4334 AN: 5156

South Asian (SAS) AF: 0.696 AC: 3345 AN: 4808

European-Finnish (FIN) AF: 0.525 AC: 5535 AN: 10542

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40632 AN: 67886

Other (OTH) AF: 0.627 AC: 1320 AN: 2106

Alfa AF: 0.610 Hom.: 10909

Bravo AF: 0.628

Asia WGS AF: 0.747 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.38
PhyloP100		-0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4529687; hg19: chr1-87614083;