Variant 15-100569187-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001040616.3(LINS1):c.*51G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 1,200,226 control chromosomes in the GnomAD database, including 4,775 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.064 ( 410 hom., cov: 31)

Exomes 𝑓: 0.087 ( 4365 hom. )

Consequence

LINS1
NM_001040616.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.40

Variant links:

Genes affected

LINS1 (HGNC:30922): (lines homolog 1) The Drosophila segment polarity gene lin encodes a protein, lines, which plays important roles in development of the epidermis and hindgut. This gene encodes a protein containing a lines-like domain. This gene is located on chromosome 15 and clustered with the gene encoding ankyrin repeat and SOCS box-containing protein 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2017]

LINS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 15-100569187-C-T is Benign according to our data. Variant chr15-100569187-C-T is described in ClinVar as [Benign]. Clinvar id is 1256652.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINS1	NM_001040616.3 linkuse as main transcript	c.*51G>A		3_prime_UTR_variant	7/7	ENST00000314742.13	NP_001035706.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINS1	ENST00000314742.13 linkuse as main transcript	c.*51G>A	3_prime_UTR_variant	7/7	5	NM_001040616.3	ENSP00000318423	P1	Q8NG48-1
LINS1	ENST00000560783.1 linkuse as main transcript	c.192-3922G>A	intron_variant, NMD_transcript_variant		5		ENSP00000474128
LINS1	ENST00000559169.1 linkuse as main transcript		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0642

AC:

9572

AN:

149058

Hom.:

409

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0191

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.0617

Gnomad ASJ

AF:

0.0566

Gnomad EAS

AF:

0.000196

Gnomad SAS

AF:

0.0395

Gnomad FIN

AF:

0.0451

Gnomad MID

AF:

0.0861

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.0723

GnomAD3 exomes

AF:

0.0627

AC:

14218

AN:

226814

Hom.:

603

AF XY:

0.0649

AC XY:

8044

AN XY:

123904

show subpopulations

Gnomad AFR exome

AF:

0.0145

Gnomad AMR exome

AF:

0.0448

Gnomad ASJ exome

AF:

0.0477

Gnomad EAS exome

AF:

0.000176

Gnomad SAS exome

AF:

0.0427

Gnomad FIN exome

AF:

0.0434

Gnomad NFE exome

AF:

0.0959

Gnomad OTH exome

AF:

0.0695

GnomAD4 exome

AF:

0.0866

AC:

91031

AN:

1051110

Hom.:

4365

Cov.:

AF XY:

0.0853

AC XY:

45893

AN XY:

538280

show subpopulations

Gnomad4 AFR exome

AF:

0.0157

Gnomad4 AMR exome

AF:

0.0470

Gnomad4 ASJ exome

AF:

0.0496

Gnomad4 EAS exome

AF:

0.000190

Gnomad4 SAS exome

AF:

0.0434

Gnomad4 FIN exome

AF:

0.0475

Gnomad4 NFE exome

AF:

0.104

Gnomad4 OTH exome

AF:

0.0781

GnomAD4 genome

AF:

0.0641

AC:

9564

AN:

149116

Hom.:

410

Cov.:

AF XY:

0.0617

AC XY:

4476

AN XY:

72560

show subpopulations

Gnomad4 AFR

AF:

0.0191

Gnomad4 AMR

AF:

0.0616

Gnomad4 ASJ

AF:

0.0566

Gnomad4 EAS

AF:

0.000197

Gnomad4 SAS

AF:

0.0394

Gnomad4 FIN

AF:

0.0451

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.0716

Alfa

AF:

0.0727

Hom.:

Bravo

AF:

0.0616

Asia WGS

AF:

0.0180

AC:

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 20, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.63

DANN

Benign

0.26

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over