15-100569122-CAAAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAA

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001040616.3(LINS1):​c.*113_*115dupTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.037 (174 hom., cov: 0)
  • Exomes 𝑓: 0.065 (13 hom.)
• Consequence: LINS1 NM_001040616.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0714 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0373 AC: 3949 AN: 105792 Hom.: 174 Cov.: 0

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.0539

Gnomad AMR AF: 0.0255

Gnomad ASJ AF: 0.0728

Gnomad EAS AF: 0.00168

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0464

Gnomad OTH AF: 0.0455

GnomAD4 exome AF: 0.0648 AC: 23508 AN: 362600 Hom.: 13 Cov.: 5 AF XY: 0.0655 AC XY: 12542 AN XY: 191454

Gnomad4 AFR exome AF: 0.0550

Gnomad4 AMR exome AF: 0.0394

Gnomad4 ASJ exome AF: 0.0677

Gnomad4 EAS exome AF: 0.0236

Gnomad4 SAS exome AF: 0.0632

Gnomad4 FIN exome AF: 0.0586

Gnomad4 NFE exome AF: 0.0724

Gnomad4 OTH exome AF: 0.0625

GnomAD4 genome AF: 0.0373 AC: 3947 AN: 105778 Hom.: 174 Cov.: 0 AF XY: 0.0354 AC XY: 1717 AN XY: 48496

Gnomad4 AFR AF: 0.0241

Gnomad4 AMR AF: 0.0255

Gnomad4 ASJ AF: 0.0728

Gnomad4 EAS AF: 0.00169

Gnomad4 SAS AF: 0.0347

Gnomad4 FIN AF: 0.0215

Gnomad4 NFE AF: 0.0464

Gnomad4 OTH AF: 0.0451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56225071; hg19: chr15-101109327;