dbSNP rs1469000: STK31:c.1714-19T>C (chr7-23770986-T-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_031414.5(STK31):c.1714-19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 1,600,556 control chromosomes in the GnomAD database, including 205,611 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 0.46 ( 16814 hom., cov: 32)

Exomes 𝑓: 0.51 ( 188797 hom. )

Consequence

STK31
NM_031414.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.621

Publications

12 publications found

Variant links:

Genes affected

STK31 (HGNC:11407): (serine/threonine kinase 31) This gene is similar to a mouse gene that encodes a putative protein kinase with a tudor domain, and shows testis-specific expression. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

STK31 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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031414.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STK31	NM_031414.5	MANE Select	c.1714-19T>C	intron	N/A	NP_113602.2
STK31	NM_001260504.2		c.1645-19T>C	intron	N/A	NP_001247433.1	A0A140VKG1
STK31	NM_001260505.2		c.1714-19T>C	intron	N/A	NP_001247434.1	Q9BXU1-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STK31	ENST00000355870.8	TSL:1 MANE Select	c.1714-19T>C	intron	N/A	ENSP00000348132.3	Q9BXU1-1
STK31	ENST00000354639.7	TSL:1	c.1645-19T>C	intron	N/A	ENSP00000346660.3	Q9BXU1-2
STK31	ENST00000405627.7	TSL:1	n.2239-19T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70473

AN:

151868

Hom.:

16801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.375

Gnomad AMI

AF:

0.520

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.424

Gnomad EAS

AF:

0.386

Gnomad SAS

AF:

0.538

Gnomad FIN

AF:

0.448

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.504

Gnomad OTH

AF:

0.458

GnomAD2 exomes

AF:

0.497

AC:

119519

AN:

240576

AF XY:

0.495

show subpopulations

Gnomad AFR exome

AF:

0.363

Gnomad AMR exome

AF:

0.642

Gnomad ASJ exome

AF:

0.435

Gnomad EAS exome

AF:

0.349

Gnomad FIN exome

AF:

0.453

Gnomad NFE exome

AF:

0.503

Gnomad OTH exome

AF:

0.495

GnomAD4 exome

AF:

0.508

AC:

735890

AN:

1448570

Hom.:

188797

Cov.:

AF XY:

0.508

AC XY:

365813

AN XY:

720422

show subpopulations

African (AFR)

AF:

0.370

AC:

12144

AN:

32800

American (AMR)

AF:

0.628

AC:

26795

AN:

42668

Ashkenazi Jewish (ASJ)

AF:

0.431

AC:

10998

AN:

25516

East Asian (EAS)

AF:

0.455

AC:

17892

AN:

39292

South Asian (SAS)

AF:

0.529

AC:

44379

AN:

83846

European-Finnish (FIN)

AF:

0.456

AC:

24167

AN:

53032

Middle Eastern (MID)

AF:

0.459

AC:

2576

AN:

5610

European-Non Finnish (NFE)

AF:

0.514

AC:

568043

AN:

1105966

Other (OTH)

AF:

0.483

AC:

28896

AN:

59840

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

15769

31538

47308

63077

78846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16492

32984

49476

65968

82460

<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:

0.464

AC:

70524

AN:

151986

Hom.:

16814

Cov.:

AF XY:

0.465

AC XY:

34525

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.375

AC:

15560

AN:

41450

American (AMR)

AF:

0.549

AC:

8374

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.424

AC:

1471

AN:

3470

East Asian (EAS)

AF:

0.386

AC:

1998

AN:

5172

South Asian (SAS)

AF:

0.541

AC:

2602

AN:

4814

European-Finnish (FIN)

AF:

0.448

AC:

4735

AN:

10576

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.504

AC:

34233

AN:

67944

Other (OTH)

AF:

0.455

AC:

959

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1903

3806

5709

7612

9515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

640

1280

1920

2560

3200

<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:

0.496

Hom.:

10706

Bravo

AF:

0.465

Asia WGS

AF:

0.469

AC:

1636

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.8

(source)

DANN

Benign

0.75

PhyloP100

0.62

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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