chr1-87159046-T-C

Variant names:

• chr1-87159046-T-C
• rs6675309
• ENST00000370548.3:c.872-9090T>C

Variant summary

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

The ENST00000370548.3(ENSG00000267561):​c.872-9090T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,086 control chromosomes in the GnomAD database, including 51,459 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 0.82 (51459 hom., cov: 30)
• Consequence: ENSG00000267561 ENST00000370548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.938
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000370548.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01140	NR_026989.1		n.336-9090T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267561	ENST00000370548.3	TSL:2	c.872-9090T>C		intron	N/A	ENSP00000359579.1
	LINC01140	ENST00000469312.6	TSL:5	n.336-6343T>C		intron	N/A
	LINC01140	ENST00000490006.6	TSL:2	n.327-9090T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124241 AN: 151968 Hom.: 51432 Cov.: 30

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.817 AC: 124325 AN: 152086 Hom.: 51459 Cov.: 30 AF XY: 0.820 AC XY: 60943 AN XY: 74342

African (AFR) AF: 0.677 AC: 28052 AN: 41446

American (AMR) AF: 0.890 AC: 13606 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2987 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5166 AN: 5170

South Asian (SAS) AF: 0.947 AC: 4549 AN: 4802

European-Finnish (FIN) AF: 0.832 AC: 8829 AN: 10608

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58322 AN: 67986

Other (OTH) AF: 0.833 AC: 1755 AN: 2108

Alfa AF: 0.833 Hom.: 9225

Bravo AF: 0.816

Asia WGS AF: 0.955 AC: 3321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.57
PhyloP100		0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6675309;

hg19: chr1-87624729;