rs2286367

Variant names:

• chr19-4664742-G-A
• rs2286367
• NM_019107.4:c.287+134C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 3 publications found

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]

ACMG classification

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	c.287+134C>T		intron_variant	Intron 3 of 5	ENST00000262947.8	NP_061980.1
MYDGF	XM_017026987.2	c.287+134C>T		intron_variant	Intron 3 of 3		XP_016882476.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20141 AN: 151874 Hom.: 3183 Cov.: 31

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

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

GnomAD4 genome AF: 0.133 AC: 20197 AN: 151992 Hom.: 3194 Cov.: 31 AF XY: 0.130 AC XY: 9646 AN XY: 74310

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: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0247 AC: 1682 AN: 67976

Other (OTH) AF: 0.110 AC: 232 AN: 2116

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
DANN	Benign	0.32
PhyloP100		-1.9
PromoterAI		0.054	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.99
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2286367; hg19: chr19-4664754; COSMIC: COSV53560878;