dbSNP rs16971872: TYRO3:c.784-88T>C (chr15-41567272-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_006293.4(TYRO3):c.784-88T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,164,046 control chromosomes in the GnomAD database, including 11,999 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 0.19 ( 3837 hom., cov: 32)

Exomes 𝑓: 0.12 ( 8162 hom. )

Consequence

TYRO3
NM_006293.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.163

Publications

4 publications found

Variant links:

Genes affected

TYRO3 (HGNC:12446): (TYRO3 protein tyrosine kinase) The gene is part of a 3-member transmembrane receptor kinase receptor family with a processed pseudogene distal on chromosome 15. The encoded protein is activated by the products of the growth arrest-specific gene 6 and protein S genes and is involved in controlling cell survival and proliferation, spermatogenesis, immunoregulation and phagocytosis. The encoded protein has also been identified as a cell entry factor for Ebola and Marburg viruses. [provided by RefSeq, May 2010]

TYRO3 links:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
TYRO3	NM_006293.4 link	c.784-88T>C	intron_variant	Intron 6 of 18	ENST00000263798.8	NP_006284.2
TYRO3	NM_001330264.2 link	c.649-88T>C	intron_variant	Intron 6 of 18		NP_001317193.1
TYRO3	XM_017022543.3 link	c.784-88T>C	intron_variant	Intron 6 of 18		XP_016878032.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
TYRO3	ENST00000263798.8 link	c.784-88T>C	intron_variant	Intron 6 of 18	1	NM_006293.4	ENSP00000263798.3
TYRO3	ENST00000559066.5 link	c.649-88T>C	intron_variant	Intron 6 of 18	5		ENSP00000454050.1
TYRO3	ENST00000560227.1 link	n.359-88T>C	intron_variant	Intron 1 of 2	5
TYRO3	ENST00000559815.1 link	n.-109T>C	upstream_gene_variant		5		ENSP00000453835.1

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

28400

AN:

151918

Hom.:

3831

Cov.:

show subpopulations

Gnomad AFR

AF:

0.381

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.0715

Gnomad EAS

AF:

0.00751

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.160

GnomAD4 exome

AF:

0.118

AC:

119036

AN:

1012010

Hom.:

8162

AF XY:

0.117

AC XY:

57830

AN XY:

494068

show subpopulations

African (AFR)

AF:

0.388

AC:

8498

AN:

21900

American (AMR)

AF:

0.123

AC:

2224

AN:

18130

Ashkenazi Jewish (ASJ)

AF:

0.0726

AC:

1091

AN:

15028

East Asian (EAS)

AF:

0.00679

AC:

205

AN:

30196

South Asian (SAS)

AF:

0.111

AC:

3619

AN:

32734

European-Finnish (FIN)

AF:

0.114

AC:

3318

AN:

29148

Middle Eastern (MID)

AF:

0.104

AC:

293

AN:

2820

European-Non Finnish (NFE)

AF:

0.116

AC:

94874

AN:

819758

Other (OTH)

AF:

0.116

AC:

4914

AN:

42296

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

4912

9824

14735

19647

24559

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3732

7464

11196

14928

18660

<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:

0.187

AC:

28439

AN:

152036

Hom.:

3837

Cov.:

AF XY:

0.184

AC XY:

13647

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.381

AC:

15777

AN:

41406

American (AMR)

AF:

0.133

AC:

2024

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0715

AC:

248

AN:

3470

East Asian (EAS)

AF:

0.00753

AC:

AN:

5178

South Asian (SAS)

AF:

0.119

AC:

574

AN:

4816

European-Finnish (FIN)

AF:

0.120

AC:

1271

AN:

10602

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.118

AC:

8002

AN:

67976

Other (OTH)

AF:

0.157

AC:

331

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1095

2190

3286

4381

5476

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.161

Hom.:

1263

Bravo

AF:

0.195

Asia WGS

AF:

0.0780

AC:

271

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.6

(source)

DANN

Benign

0.62

PhyloP100

-0.16

Mutation Taster

=100/0

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