Variant chr15-100569122-C-CAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001040616.3(LINS1):c.*115_*116insTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.36 ( 7309 hom., cov: 0)

Exomes 𝑓: 0.24 ( 157 hom. )

Consequence

LINS1
NM_001040616.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.597

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 15-100569122-C-CAA is Benign according to our data. Variant chr15-100569122-C-CAA is described in ClinVar as [Benign]. Clinvar id is 1281296.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINS1	NM_001040616.3 linkuse as main transcript	c.115_116insTT		3_prime_UTR_variant	7/7	ENST00000314742.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINS1	ENST00000314742.13 linkuse as main transcript	c.115_116insTT		3_prime_UTR_variant	7/7	5	NM_001040616.3	P1	Q8NG48-1
LINS1	ENST00000560783.1 linkuse as main transcript	c.192-3858_192-3857insTT		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.358

AC:

37809

AN:

105592

Hom.:

7314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.370

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.323

Gnomad EAS

AF:

0.297

Gnomad SAS

AF:

0.311

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.319

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.334

GnomAD4 exome

AF:

0.240

AC:

86373

AN:

360468

Hom.:

157

Cov.:

AF XY:

0.240

AC XY:

45757

AN XY:

190336

show subpopulations

Gnomad4 AFR exome

AF:

0.219

Gnomad4 AMR exome

AF:

0.173

Gnomad4 ASJ exome

AF:

0.200

Gnomad4 EAS exome

AF:

0.143

Gnomad4 SAS exome

AF:

0.235

Gnomad4 FIN exome

AF:

0.231

Gnomad4 NFE exome

AF:

0.260

Gnomad4 OTH exome

AF:

0.231

GnomAD4 genome

AF:

0.358

AC:

37794

AN:

105578

Hom.:

7309

Cov.:

AF XY:

0.354

AC XY:

17124

AN XY:

48366

show subpopulations

Gnomad4 AFR

AF:

0.343

Gnomad4 AMR

AF:

0.232

Gnomad4 ASJ

AF:

0.323

Gnomad4 EAS

AF:

0.297

Gnomad4 SAS

AF:

0.310

Gnomad4 FIN

AF:

0.304

Gnomad4 NFE

AF:

0.398

Gnomad4 OTH

AF:

0.331

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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