chr15-100569122-CA-C

Variant names:

• chr15-100569122-CA-C
• rs56225071
• NM_001040616.3:c.*115delT

Variant summary

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

The NM_001040616.3(LINS1):​c.*115delT 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 0.00019 (0 hom., cov: 0)
  • Exomes 𝑓: 0.049 (0 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 (EAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.000188 AC: 20 AN: 106106 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000363

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000108

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00167

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00165

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000145

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0492 AC: 17687 AN: 359446 Hom.: 0 Cov.: 5 AF XY: 0.0489 AC XY: 9270 AN XY: 189736

Gnomad4 AFR exome AF: 0.0449

Gnomad4 AMR exome AF: 0.0570

Gnomad4 ASJ exome AF: 0.0588

Gnomad4 EAS exome AF: 0.124

Gnomad4 SAS exome AF: 0.0437

Gnomad4 FIN exome AF: 0.0508

Gnomad4 NFE exome AF: 0.0406

Gnomad4 OTH exome AF: 0.0525

GnomAD4 genome AF: 0.000189 AC: 20 AN: 106092 Hom.: 0 Cov.: 0 AF XY: 0.000247 AC XY: 12 AN XY: 48626

Gnomad4 AFR AF: 0.0000363

Gnomad4 AMR AF: 0.000108

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00168

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00165

Gnomad4 NFE AF: 0.000145

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs56225071; hg19: chr15-101109327;