Genetic Variant MYDGF:c.287+134C>T (chr19-4664742-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_019107.4(MYDGF):c.287+134C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 945,806 control chromosomes in the GnomAD database, including 5,562 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 0.13 ( 3194 hom., cov: 31)

Exomes 𝑓: 0.042 ( 2368 hom. )

Consequence

MYDGF
NM_019107.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.92

Publications

3 publications found

Variant links:

Genes affected

MYDGF (HGNC:16948): (myeloid derived growth factor) The protein encoded by this gene was previously thought to support proliferation of lymphoid cells and was considered an interleukin. However, this activity has not been reproducible and the function of this protein is currently unknown. [provided by RefSeq, Jul 2008]

MYDGF 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYDGF	NM_019107.4 link	c.287+134C>T		intron_variant	Intron 3 of 5	ENST00000262947.8	NP_061980.1	Q969H8
MYDGF	XM_017026987.2 link	c.287+134C>T		intron_variant	Intron 3 of 3		XP_016882476.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MYDGF	ENST00000262947.8 link	c.287+134C>T	intron_variant	Intron 3 of 5	1	NM_019107.4	ENSP00000262947.2	Q969H8
MYDGF	ENST00000599630.1 link	c.287+134C>T	intron_variant	Intron 3 of 4	2		ENSP00000469945.1	M0QYN0
MYDGF	ENST00000599761.5 link	c.29+134C>T	intron_variant	Intron 1 of 3	3		ENSP00000469136.1	M0QXF7
MYDGF	ENST00000596031.1 link	n.164+134C>T	intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20141

AN:

151874

Hom.:

3183

Cov.:

show subpopulations

Gnomad AFR

AF:

0.383

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.0623

Gnomad ASJ

AF:

0.0579

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.0740

Gnomad FIN

AF:

0.0122

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.0247

Gnomad OTH

AF:

0.110

GnomAD4 exome

AF:

0.0419

AC:

33267

AN:

793814

Hom.:

2368

AF XY:

0.0417

AC XY:

16669

AN XY:

399648

show subpopulations

African (AFR)

AF:

0.400

AC:

7653

AN:

19152

American (AMR)

AF:

0.0401

AC:

1007

AN:

25132

Ashkenazi Jewish (ASJ)

AF:

0.0613

AC:

975

AN:

15912

East Asian (EAS)

AF:

0.137

AC:

4239

AN:

30928

South Asian (SAS)

AF:

0.0658

AC:

3604

AN:

54792

European-Finnish (FIN)

AF:

0.0102

AC:

333

AN:

32686

Middle Eastern (MID)

AF:

0.108

AC:

354

AN:

3292

European-Non Finnish (NFE)

AF:

0.0223

AC:

12810

AN:

575372

Other (OTH)

AF:

0.0627

AC:

2292

AN:

36548

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1360

2721

4081

5442

6802

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

540

1080

1620

2160

2700

<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:

0.133

AC:

20197

AN:

151992

Hom.:

3194

Cov.:

AF XY:

0.130

AC XY:

9646

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.383

AC:

15844

AN:

41392

American (AMR)

AF:

0.0621

AC:

950

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0579

AC:

201

AN:

3472

East Asian (EAS)

AF:

0.140

AC:

719

AN:

5140

South Asian (SAS)

AF:

0.0740

AC:

357

AN:

4822

European-Finnish (FIN)

AF:

0.0122

AC:

129

AN:

10580

Middle Eastern (MID)

AF:

0.0959

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0247

AC:

1682

AN:

67976

Other (OTH)

AF:

0.110

AC:

232

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

715

1430

2146

2861

3576

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.0850

Hom.:

220

Bravo

AF:

0.147

Asia WGS

AF:

0.137

AC:

478

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.016

(source)

DANN

Benign

0.32

PhyloP100

-1.9

PromoterAI

0.054

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.99

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