Genetic Variant NM_201412.3:c.807-146T>G (chr16-190281-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Publications

34 publications found

Variant links:

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]

LUC7L links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LUC7L	NM_201412.3	MANE Select	c.807-146T>G	intron	N/A	NP_958815.1
LUC7L	NM_001320226.2		c.807-146T>G	intron	N/A	NP_001307155.1
LUC7L	NM_018032.5		c.807-146T>G	intron	N/A	NP_060502.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LUC7L	ENST00000293872.13	TSL:1 MANE Select	c.807-146T>G	intron	N/A	ENSP00000293872.8
LUC7L	ENST00000337351.8	TSL:1	c.807-146T>G	intron	N/A	ENSP00000337507.4
LUC7L	ENST00000426094.5	TSL:1	n.*1970-146T>G	intron	N/A	ENSP00000390953.1

Frequencies

GnomAD3 genomes

AF:

0.655

AC:

99211

AN:

151386

Hom.:

32688

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.726

AC:

11225

AN:

15470

American (AMR)

AF:

0.685

AC:

13995

AN:

20424

Ashkenazi Jewish (ASJ)

AF:

0.607

AC:

9128

AN:

15040

East Asian (EAS)

AF:

0.529

AC:

16954

AN:

32068

South Asian (SAS)

AF:

0.655

AC:

33235

AN:

50730

European-Finnish (FIN)

AF:

0.612

AC:

25817

AN:

42156

Middle Eastern (MID)

AF:

0.625

AC:

2427

AN:

3882

European-Non Finnish (NFE)

AF:

0.641

AC:

269699

AN:

420766

Other (OTH)

AF:

0.635

AC:

20397

AN:

32134

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

7792

15584

23377

31169

38961

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4166

8332

12498

16664

20830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.655

AC:

99290

AN:

151504

Hom.:

32714

Cov.:

AF XY:

0.651

AC XY:

48179

AN XY:

73992

show subpopulations

African (AFR)

AF:

0.721

AC:

29749

AN:

41268

American (AMR)

AF:

0.640

AC:

9704

AN:

15172

Ashkenazi Jewish (ASJ)

AF:

0.606

AC:

2103

AN:

3470

East Asian (EAS)

AF:

0.514

AC:

2637

AN:

5126

South Asian (SAS)

AF:

0.650

AC:

3124

AN:

4804

European-Finnish (FIN)

AF:

0.609

AC:

6354

AN:

10434

Middle Eastern (MID)

AF:

0.671

AC:

196

AN:

292

European-Non Finnish (NFE)

AF:

0.640

AC:

43443

AN:

67918

Other (OTH)

AF:

0.641

AC:

1351

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1717

3435

5152

6870

8587

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

796

1592

2388

3184

3980

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.644

Hom.:

62970

Bravo

AF:

0.661

Asia WGS

AF:

0.616

AC:

2143

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.13

(source)

DANN

Benign

0.46

PhyloP100

-1.4

PromoterAI

0.021

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over