Genetic Variant TYRO3:c.668-144A>T (chr15-41564882-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_006293.4(TYRO3):c.668-144A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TYRO3
NM_006293.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.457

Publications

0 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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TYRO3	NM_006293.4 link	c.668-144A>T	intron_variant	Intron 5 of 18	ENST00000263798.8	NP_006284.2	Q06418
TYRO3	NM_001330264.2 link	c.533-144A>T	intron_variant	Intron 5 of 18		NP_001317193.1	Q06418H0YNK6
TYRO3	XM_017022543.3 link	c.668-144A>T	intron_variant	Intron 5 of 18		XP_016878032.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TYRO3	ENST00000263798.8 link	c.668-144A>T	intron_variant	Intron 5 of 18	1	NM_006293.4	ENSP00000263798.3	Q06418
TYRO3	ENST00000560227.1 link	n.99A>T	non_coding_transcript_exon_variant	Exon 1 of 3	5
TYRO3	ENST00000559066.5 link	c.533-144A>T	intron_variant	Intron 5 of 18	5		ENSP00000454050.1	H0YNK6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

486086

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

257600

African (AFR)

AF:

0.00

AC:

AN:

14488

American (AMR)

AF:

0.00

AC:

AN:

30544

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15876

East Asian (EAS)

AF:

0.00

AC:

AN:

30766

South Asian (SAS)

AF:

0.00

AC:

AN:

52214

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31550

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2110

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

281052

Other (OTH)

AF:

0.00

AC:

AN:

27486

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.85

(source)

DANN

Benign

0.45

PhyloP100

-0.46

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

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over