NM_201412.3:c.255+5489G>A

Variant names:

• chr16-215160-C-T
• rs1203981
• NM_201412.3:c.255+5489G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201412.3(LUC7L):​c.255+5489G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,982 control chromosomes in the GnomAD database, including 28,309 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 0.61 (28309 hom., cov: 32)
• Consequence: LUC7L NM_201412.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201412.3. 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
	LUC7L	NM_201412.3	MANE Select	c.255+5489G>A		intron	N/A	NP_958815.1	Q9NQ29-1
	LUC7L	NM_001320226.2		c.255+5489G>A		intron	N/A	NP_001307155.1	Q9NQ29-2
	LUC7L	NM_018032.5		c.255+5489G>A		intron	N/A	NP_060502.1	Q9NQ29-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LUC7L	ENST00000293872.13	TSL:1 MANE Select	c.255+5489G>A		intron	N/A	ENSP00000293872.8	Q9NQ29-1
	LUC7L	ENST00000337351.8	TSL:1	c.255+5489G>A		intron	N/A	ENSP00000337507.4	Q9NQ29-2
	LUC7L	ENST00000426094.5	TSL:1	n.*1418+5489G>A		intron	N/A	ENSP00000390953.1	F8WBC1

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92009 AN: 151864 Hom.: 28276 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.623

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.606 AC: 92099 AN: 151982 Hom.: 28309 Cov.: 32 AF XY: 0.608 AC XY: 45171 AN XY: 74268

African (AFR) AF: 0.700 AC: 29029 AN: 41472

American (AMR) AF: 0.596 AC: 9085 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1941 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3504 AN: 5154

South Asian (SAS) AF: 0.657 AC: 3163 AN: 4814

European-Finnish (FIN) AF: 0.558 AC: 5892 AN: 10552

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.553 AC: 37554 AN: 67964

Other (OTH) AF: 0.627 AC: 1324 AN: 2110

Alfa AF: 0.591 Hom.: 20089

Bravo AF: 0.613

Asia WGS AF: 0.685 AC: 2385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.25
DANN	Benign	0.46
PhyloP100		-0.17
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs1203981; hg19: chr16-265159;