chr1-87146027-A-G

Variant names:

• chr1-87146027-A-G
• rs719015
• ENST00000370548.3:c.871+12309A>G

Variant summary

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

The ENST00000370548.3(ENSG00000267561):​c.871+12309A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,048 control chromosomes in the GnomAD database, including 25,571 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 0.57 (25571 hom., cov: 32)
• Consequence: ENSG00000267561 ENST00000370548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 11 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01140	NR_026989.1	n.335+12309A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267561	ENST00000370548.3	c.871+12309A>G		intron_variant	Intron 7 of 7	2		ENSP00000359579.1
LINC01140	ENST00000469312.6	n.335+12309A>G		intron_variant	Intron 2 of 3	5
LINC01140	ENST00000490006.6	n.326+12309A>G		intron_variant	Intron 2 of 2	2
LINC01140	ENST00000587165.1	n.310+12309A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87150 AN: 151930 Hom.: 25564 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.573 AC: 87191 AN: 152048 Hom.: 25571 Cov.: 32 AF XY: 0.575 AC XY: 42750 AN XY: 74316

African (AFR) AF: 0.475 AC: 19691 AN: 41452

American (AMR) AF: 0.671 AC: 10251 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4322 AN: 5170

South Asian (SAS) AF: 0.692 AC: 3339 AN: 4828

European-Finnish (FIN) AF: 0.521 AC: 5496 AN: 10552

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39898 AN: 67976

Other (OTH) AF: 0.599 AC: 1265 AN: 2112

Alfa AF: 0.590 Hom.: 113707

Bravo AF: 0.583

Asia WGS AF: 0.725 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.84
PhyloP100		0.056

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: rs719015; hg19: chr1-87611710; COSMIC: COSV65206840;