21-38397191-T-C

Variant names:

• chr21-38397191-T-C
• rs2836368
• NM_182918.4:c.745+3383A>G

Variant summary

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

The NM_182918.4(ERG):​c.745+3383A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,042 control chromosomes in the GnomAD database, including 5,823 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 0.26 (5823 hom., cov: 31)
• Consequence: ERG NM_182918.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 3 publications found

Genes affected

ERG (HGNC:3446): (ETS transcription factor ERG) This gene encodes a member of the erythroblast transformation-specific (ETS) family of transcriptions factors. All members of this family are key regulators of embryonic development, cell proliferation, differentiation, angiogenesis, inflammation, and apoptosis. The protein encoded by this gene is mainly expressed in the nucleus. It contains an ETS DNA-binding domain and a PNT (pointed) domain which is implicated in the self-association of chimeric oncoproteins. This protein is required for platelet adhesion to the subendothelium, inducing vascular cell remodeling. It also regulates hematopoesis, and the differentiation and maturation of megakaryocytic cells. This gene is involved in chromosomal translocations, resulting in different fusion gene products, such as TMPSSR2-ERG and NDRG1-ERG in prostate cancer, EWS-ERG in Ewing's sarcoma and FUS-ERG in acute myeloid leukemia. More than two dozens of transcript variants generated from combinatorial usage of three alternative promoters and multiple alternative splicing events have been reported, but the full-length nature of many of these variants has not been determined. [provided by RefSeq, Apr 2014]

ERG Gene-Disease associations (from GenCC):

• lymphatic malformation 14

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182918.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERG	NM_182918.4	MANE Select	c.745+3383A>G		intron	N/A	NP_891548.1	P11308-4
	ERG	NM_001136154.1		c.766+3383A>G		intron	N/A	NP_001129626.1	P11308-3
	ERG	NM_001243428.1		c.766+3383A>G		intron	N/A	NP_001230357.1	P11308-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERG	ENST00000288319.12	TSL:1 MANE Select	c.745+3383A>G		intron	N/A	ENSP00000288319.7	P11308-4
	ERG	ENST00000398919.6	TSL:1	c.766+3383A>G		intron	N/A	ENSP00000381891.2	P11308-3
	ERG	ENST00000398905.5	TSL:1	c.674-4747A>G		intron	N/A	ENSP00000381877.1	B5MDW0

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39151 AN: 151924 Hom.: 5814 Cov.: 31

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.268

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.258 AC: 39189 AN: 152042 Hom.: 5823 Cov.: 31 AF XY: 0.258 AC XY: 19206 AN XY: 74308

African (AFR) AF: 0.0973 AC: 4035 AN: 41488

American (AMR) AF: 0.335 AC: 5121 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 962 AN: 3468

East Asian (EAS) AF: 0.269 AC: 1385 AN: 5156

South Asian (SAS) AF: 0.364 AC: 1752 AN: 4816

European-Finnish (FIN) AF: 0.271 AC: 2867 AN: 10566

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22056 AN: 67958

Other (OTH) AF: 0.272 AC: 574 AN: 2114

Alfa AF: 0.187 Hom.: 667

Bravo AF: 0.254

Asia WGS AF: 0.320 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.068
DANN	Benign	0.51
PhyloP100		-0.81
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: rs2836368; hg19: chr21-39769113;