chr1-87147675-T-C

Variant names:

• chr1-87147675-T-C
• rs7553864
• ENST00000370548.3:c.871+13957T>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+13957T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,010 control chromosomes in the GnomAD database, including 28,014 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 0.60 (28014 hom., cov: 32)
• Consequence: ENSG00000267561 ENST00000370548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• Publications: 13 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01140	NR_026989.1		n.335+13957T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267561	ENST00000370548.3	TSL:2	c.871+13957T>C		intron	N/A	ENSP00000359579.1
	LINC01140	ENST00000469312.6	TSL:5	n.335+13957T>C		intron	N/A
	LINC01140	ENST00000490006.6	TSL:2	n.326+13957T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91683 AN: 151892 Hom.: 28004 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.603 AC: 91737 AN: 152010 Hom.: 28014 Cov.: 32 AF XY: 0.604 AC XY: 44884 AN XY: 74318

African (AFR) AF: 0.560 AC: 23218 AN: 41446

American (AMR) AF: 0.676 AC: 10334 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2085 AN: 3468

East Asian (EAS) AF: 0.840 AC: 4333 AN: 5158

South Asian (SAS) AF: 0.702 AC: 3378 AN: 4814

European-Finnish (FIN) AF: 0.526 AC: 5562 AN: 10568

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40714 AN: 67958

Other (OTH) AF: 0.615 AC: 1298 AN: 2110

Alfa AF: 0.610 Hom.: 122030

Bravo AF: 0.615

Asia WGS AF: 0.745 AC: 2590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		-0.90

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: rs7553864; hg19: chr1-87613358;