15-100569122-CAAAAAAAAAAAAAA-CAAAAAAAAAAA

Variant names:

• chr15-100569122-CAAA-C
• rs56225071
• NM_001040616.3:c.*113_*115delTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001040616.3(LINS1):​c.*113_*115delTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0025 in 474,252 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00012 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0032 (0 hom.)
• Consequence: LINS1 NM_001040616.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• intellectual disability, autosomal recessive 27

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• autosomal recessive non-syndromic intellectual disability

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINS1	NM_001040616.3	c.*113_*115delTTT		3_prime_UTR_variant	Exon 7 of 7	ENST00000314742.13	NP_001035706.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINS1	ENST00000314742.13	c.*113_*115delTTT		3_prime_UTR_variant	Exon 7 of 7	5	NM_001040616.3	ENSP00000318423.8
LINS1	ENST00000560783.1	n.191-3860_191-3858delTTT		intron_variant	Intron 1 of 3	5		ENSP00000474128.1
LINS1	ENST00000559169.1	n.*110_*112delTTT		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.000123 AC: 13 AN: 106106 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000363

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000661

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000182

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00318 AC: 1171 AN: 368160 Hom.: 0 AF XY: 0.00314 AC XY: 610 AN XY: 194406

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00438 AC: 46 AN: 10512

American (AMR) AF: 0.00420 AC: 61 AN: 14538

Ashkenazi Jewish (ASJ) AF: 0.00450 AC: 48 AN: 10658

East Asian (EAS) AF: 0.00567 AC: 142 AN: 25026

South Asian (SAS) AF: 0.00183 AC: 68 AN: 37110

European-Finnish (FIN) AF: 0.00263 AC: 53 AN: 20130

Middle Eastern (MID) AF: 0.00398 AC: 6 AN: 1506

European-Non Finnish (NFE) AF: 0.00294 AC: 671 AN: 228464

Other (OTH) AF: 0.00376 AC: 76 AN: 20216

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.000123 AC: 13 AN: 106092 Hom.: 0 Cov.: 0 AF XY: 0.000103 AC XY: 5 AN XY: 48628

African (AFR) AF: 0.000363 AC: 10 AN: 27570

American (AMR) AF: 0.00 AC: 0 AN: 9300

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2882

East Asian (EAS) AF: 0.00 AC: 0 AN: 2972

South Asian (SAS) AF: 0.00 AC: 0 AN: 2948

European-Finnish (FIN) AF: 0.000661 AC: 2 AN: 3028

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 192

European-Non Finnish (NFE) AF: 0.0000182 AC: 1 AN: 55044

Other (OTH) AF: 0.00 AC: 0 AN: 1356

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.60

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: rs56225071; hg19: chr15-101109327;