NM_001040616.3:c.*110_*115delTTTTTT

Variant names:

• chr15-100569122-CAAAAAA-C
• rs56225071
• NM_001040616.3:c.*110_*115delTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001040616.3(LINS1):​c.*110_*115delTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000189 in 371,298 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 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000019 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINS1 NM_001040616.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• 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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040616.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINS1	NM_001040616.3	MANE Select	c.*110_*115delTTTTTT		3_prime_UTR	Exon 7 of 7	NP_001035706.2	Q8NG48-1
	LINS1	NM_001352508.2		c.*110_*115delTTTTTT		3_prime_UTR	Exon 7 of 7	NP_001339437.1
	LINS1	NM_001352507.2		c.*110_*115delTTTTTT		3_prime_UTR	Exon 8 of 8	NP_001339436.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINS1	ENST00000314742.13	TSL:5 MANE Select	c.*110_*115delTTTTTT		3_prime_UTR	Exon 7 of 7	ENSP00000318423.8	Q8NG48-1
	LINS1	ENST00000869606.1		c.*110_*115delTTTTTT		3_prime_UTR	Exon 7 of 7	ENSP00000539665.1
	LINS1	ENST00000869607.1		c.*110_*115delTTTTTT		3_prime_UTR	Exon 7 of 7	ENSP00000539666.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 106108 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

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: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000189 AC: 7 AN: 371298 Hom.: 0 AF XY: 0.0000306 AC XY: 6 AN XY: 196032

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

African (AFR) AF: 0.0000943 AC: 1 AN: 10602

American (AMR) AF: 0.0000680 AC: 1 AN: 14712

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10748

East Asian (EAS) AF: 0.0000394 AC: 1 AN: 25408

South Asian (SAS) AF: 0.00 AC: 0 AN: 37456

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20292

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1514

European-Non Finnish (NFE) AF: 0.00000869 AC: 2 AN: 230132

Other (OTH) AF: 0.0000979 AC: 2 AN: 20434

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 106108 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 48624

African (AFR) AF: 0.00 AC: 0 AN: 27544

American (AMR) AF: 0.00 AC: 0 AN: 9288

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 2986

South Asian (SAS) AF: 0.00 AC: 0 AN: 2972

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3028

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 210

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 55056

Other (OTH) AF: 0.00 AC: 0 AN: 1342

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs56225071; hg19: chr15-101109327;