rs1211375

chr16-190281-A-Cchr16-190281-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201412.3(LUC7L):c.807-146T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 784,174 control chromosomes in the GnomAD database, including 162,383 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.66 (32714 hom., cov: 28)
  • Exomes 𝑓: 0.64 (129669 hom.)
• Consequence: LUC7L NM_201412.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

LUC7L (HGNC:6723): (LUC7 like) The LUC7L gene may represent a mammalian heterochromatic gene, encoding a putative RNA-binding protein similar to the yeast Luc7p subunit of the U1 snRNP splicing complex that is normally required for 5-prime splice site selection (Tufarelli et al., 2001 [PubMed 11170747]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LUC7L	NM_201412.3	c.807-146T>G		intron_variant		ENST00000293872.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LUC7L	ENST00000293872.13	c.807-146T>G		intron_variant		1	NM_201412.3	P1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99211 AN: 151386 Hom.: 32688 Cov.: 28

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.637 AC: 402877 AN: 632670 Hom.: 129669 AF XY: 0.638 AC XY: 207853 AN XY: 325840

Gnomad4 AFR exome AF: 0.726

Gnomad4 AMR exome AF: 0.685

Gnomad4 ASJ exome AF: 0.607

Gnomad4 EAS exome AF: 0.529

Gnomad4 SAS exome AF: 0.655

Gnomad4 FIN exome AF: 0.612

Gnomad4 NFE exome AF: 0.641

Gnomad4 OTH exome AF: 0.635

GnomAD4 genome AF: 0.655 AC: 99290 AN: 151504 Hom.: 32714 Cov.: 28 AF XY: 0.651 AC XY: 48179 AN XY: 73992

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.641

Alfa AF: 0.638 Hom.: 13569

Bravo AF: 0.661

Asia WGS AF: 0.616 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.13
Dann	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1211375; hg19: chr16-240280; COSMIC: COSV53460289; COSMIC: COSV53460289;