dbSNP rs17057781: SLU7:c.-61T>C (chr5-160419067-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006425.5(SLU7):c.-61T>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,284 control chromosomes in the GnomAD database, including 1,585 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 0.14 ( 1584 hom., cov: 32)

Exomes 𝑓: 0.17 ( 1 hom. )

Consequence

SLU7
NM_006425.5 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.141

Publications

17 publications found

Variant links:

Genes affected

SLU7 (HGNC:16939): (SLU7 homolog, splicing factor) Pre-mRNA splicing occurs in two sequential transesterification steps. The protein encoded by this gene is a splicing factor that has been found to be essential during the second catalytic step in the pre-mRNA splicing process. It associates with the spliceosome and contains a zinc knuckle motif that is found in other splicing factors and is involved in protein-nucleic acid and protein-protein interactions. [provided by RefSeq, Jul 2008]

SLU7 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=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLU7	NM_006425.5 link	c.-61T>C		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 16	ENST00000297151.9	NP_006416.3
SLU7	NM_006425.5 link	c.-61T>C		5_prime_UTR_variant	Exon 1 of 16	ENST00000297151.9	NP_006416.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLU7	ENST00000297151.9 link	c.-61T>C		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 16	1	NM_006425.5	ENSP00000297151.4
SLU7	ENST00000297151.9 link	c.-61T>C		5_prime_UTR_variant	Exon 1 of 16	1	NM_006425.5	ENSP00000297151.4

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21569

AN:

152136

Hom.:

1584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.205

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.158

GnomAD4 exome

AF:

0.167

AC:

AN:

Hom.:

Cov.:

AF XY:

0.150

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.167

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.408

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.142

AC:

21579

AN:

152254

Hom.:

1584

Cov.:

AF XY:

0.142

AC XY:

10538

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.126

AC:

5234

AN:

41552

American (AMR)

AF:

0.102

AC:

1568

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

562

AN:

3470

East Asian (EAS)

AF:

0.206

AC:

1064

AN:

5174

South Asian (SAS)

AF:

0.199

AC:

959

AN:

4824

European-Finnish (FIN)

AF:

0.154

AC:

1627

AN:

10588

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.146

AC:

9952

AN:

68016

Other (OTH)

AF:

0.157

AC:

332

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

979

1957

2936

3914

4893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.145

Hom.:

2137

Bravo

AF:

0.137

Asia WGS

AF:

0.207

AC:

721

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

6.0

(source)

DANN

Benign

0.42

PhyloP100

0.14

PromoterAI

0.14

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over