Genetic Variant PRDM16:c.37+23_37+55delCGCCGCGCCGCCGGGGCCCGGGCCGCCGGGCCG (chr1-3069313-CGGCCGCGCCGCGCCGCCGGGGCCCGGGCCGCCG-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_022114.4(PRDM16):c.37+23_37+55delCGCCGCGCCGCCGGGGCCCGGGCCGCCGGGCCG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000167 in 1,200,814 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 27)

Exomes 𝑓: 0.0000017 ( 0 hom. )

Consequence

PRDM16
NM_022114.4 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.71

Publications

0 publications found

Variant links:

Genes affected

PRDM16 (HGNC:14000): (PR/SET domain 16) The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). This gene is located near the 1p36.3 breakpoint and has been shown to be specifically expressed in the t(1:3)(p36,q21)-positive MDS/AML. The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal PR domain. The translocation results in the overexpression of a truncated version of this protein that lacks the PR domain, which may play an important role in the pathogenesis of MDS and AML. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

PRDM16 links:

PRDM16-DT (HGNC:48664): (PRDM16 divergent transcript)

PRDM16-DT links:

LOC124903827 (HGNC:):

LOC124903827 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP6

Variant 1-3069313-CGGCCGCGCCGCGCCGCCGGGGCCCGGGCCGCCG-C is Benign according to our data. Variant chr1-3069313-CGGCCGCGCCGCGCCGCCGGGGCCCGGGCCGCCG-C is described in ClinVar as [Likely_benign]. Clinvar id is 1943324.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDM16	NM_022114.4 link	c.37+23_37+55delCGCCGCGCCGCCGGGGCCCGGGCCGCCGGGCCG		intron_variant	Intron 1 of 16	ENST00000270722.10	NP_071397.3	Q9HAZ2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDM16	ENST00000270722.10 link	c.37+18_37+50delGGCCGCGCCGCGCCGCCGGGGCCCGGGCCGCCG		intron_variant	Intron 1 of 16	1	NM_022114.4	ENSP00000270722.5		Q9HAZ2-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

157718

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000167

AC:

AN:

1200814

Hom.:

AF XY:

0.00000338

AC XY:

AN XY:

591616

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24940

American (AMR)

AF:

0.00

AC:

AN:

27772

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18438

East Asian (EAS)

AF:

0.00

AC:

AN:

24176

South Asian (SAS)

AF:

0.0000340

AC:

AN:

58848

European-Finnish (FIN)

AF:

0.00

AC:

AN:

36074

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3608

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

961690

Other (OTH)

AF:

0.00

AC:

AN:

45268

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.800

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Left ventricular noncompaction 8

Benign:1

Jun 11, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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chr1-3069313-CGGCCGCGCCGCGCCGCCGGGGCCCGGGCCGCCG-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over