rs2286367

Positions:

• chr19-4664742-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MYDGF	NM_019107.4	c.287+134C>T		intron_variant		ENST00000262947.8
MYDGF	XM_017026987.2	c.287+134C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYDGF	ENST00000262947.8	c.287+134C>T		intron_variant		1	NM_019107.4	P1
MYDGF	ENST00000599630.1	c.287+134C>T		intron_variant		2
MYDGF	ENST00000599761.5	c.31+134C>T		intron_variant		3
MYDGF	ENST00000596031.1	n.164+134C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR exome AF: 0.400

Gnomad4 AMR exome AF: 0.0401

Gnomad4 ASJ exome AF: 0.0613

Gnomad4 EAS exome AF: 0.137

Gnomad4 SAS exome AF: 0.0658

Gnomad4 FIN exome AF: 0.0102

Gnomad4 NFE exome AF: 0.0223

Gnomad4 OTH exome AF: 0.0627

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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.0621

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.0122

Gnomad4 NFE AF: 0.0247

Gnomad4 OTH AF: 0.110

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
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.99

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

LitVar

Other links and lift over

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