1-87147675-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026989.1(LINC01140):n.335+13957T>C variant causes a intron, non coding transcript 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: LINC01140 NR_026989.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01140	NR_026989.1	n.335+13957T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01140	ENST00000490006.6	n.326+13957T>C		intron_variant, non_coding_transcript_variant		2
LINC01140	ENST00000469312.6	n.335+13957T>C		intron_variant, non_coding_transcript_variant		5
LINC01140	ENST00000587165.1	n.310+13957T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.615

Alfa AF: 0.612 Hom.: 62066

Bravo AF: 0.615

Asia WGS AF: 0.745 AC: 2590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	11
Dann	Benign	0.84

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

Publications

LitVar

Other links and lift over

dbSNP: rs7553864; hg19: chr1-87613358;