dbSNP rs11684598: MYADML:n.654C>T (chr2-33727554-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 ENST00000474610.1(MYADML):n.654C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 1,271,480 control chromosomes in the GnomAD database, including 139,827 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 0.46 ( 16271 hom., cov: 33)

Exomes 𝑓: 0.47 ( 123556 hom. )

Consequence

MYADML
ENST00000474610.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.929

Publications

12 publications found

Variant links:

Genes affected

MYADML (HGNC:):

MYADML links:

MYADML (HGNC:31019): (myeloid associated differentiation marker like (pseudogene))

MYADML links:

LINC01320 (HGNC:50526): (long intergenic non-protein coding RNA 1320)

LINC01320 links:

LINC01317 (HGNC:50523): (long intergenic non-protein coding RNA 1317)

LINC01317 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=-0.53).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYADML	NR_003143.2 link	n.664C>T		non_coding_transcript_exon_variant	Exon 1 of 1
LINC01317	NR_126403.1 link	n.68+20601G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MYADML	ENST00000474610.1 link	n.654C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
MYADML	ENST00000490394.1 link	n.11C>T	non_coding_transcript_exon_variant	Exon 1 of 3	3
MYADML	ENST00000491596.1 link	n.435C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.455

AC:

69176

AN:

151914

Hom.:

16267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.345

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.547

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.438

Gnomad SAS

AF:

0.479

Gnomad FIN

AF:

0.520

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.496

Gnomad OTH

AF:

0.432

GnomAD2 exomes

AF:

0.488

AC:

115834

AN:

237342

AF XY:

0.488

show subpopulations

Gnomad AFR exome

AF:

0.338

Gnomad AMR exome

AF:

0.588

Gnomad ASJ exome

AF:

0.404

Gnomad EAS exome

AF:

0.433

Gnomad FIN exome

AF:

0.531

Gnomad NFE exome

AF:

0.493

Gnomad OTH exome

AF:

0.472

GnomAD4 exome

AF:

0.468

AC:

523375

AN:

1119448

Hom.:

123556

Cov.:

AF XY:

0.469

AC XY:

268042

AN XY:

571532

show subpopulations

African (AFR)

AF:

0.317

AC:

8763

AN:

27634

American (AMR)

AF:

0.581

AC:

25341

AN:

43600

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

9455

AN:

23730

East Asian (EAS)

AF:

0.461

AC:

17322

AN:

37600

South Asian (SAS)

AF:

0.475

AC:

37921

AN:

79760

European-Finnish (FIN)

AF:

0.525

AC:

20027

AN:

38138

Middle Eastern (MID)

AF:

0.437

AC:

2234

AN:

5108

European-Non Finnish (NFE)

AF:

0.467

AC:

380228

AN:

814978

Other (OTH)

AF:

0.452

AC:

22084

AN:

48900

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

Heterozygous variant carriers

11250

22500

33751

45001

56251

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9726

19452

29178

38904

48630

<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:

0.455

AC:

69203

AN:

152032

Hom.:

16271

Cov.:

AF XY:

0.461

AC XY:

34248

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.345

AC:

14301

AN:

41500

American (AMR)

AF:

0.547

AC:

8369

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.399

AC:

1385

AN:

3472

East Asian (EAS)

AF:

0.439

AC:

2248

AN:

5126

South Asian (SAS)

AF:

0.481

AC:

2320

AN:

4820

European-Finnish (FIN)

AF:

0.520

AC:

5488

AN:

10562

Middle Eastern (MID)

AF:

0.452

AC:

133

AN:

294

European-Non Finnish (NFE)

AF:

0.496

AC:

33727

AN:

67940

Other (OTH)

AF:

0.435

AC:

919

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1916

3832

5749

7665

9581

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

644

1288

1932

2576

3220

<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:

0.474

Hom.:

19781

Bravo

AF:

0.446

Asia WGS

AF:

0.437

AC:

1523

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

0.36

(source)

DANN

Benign

0.86

PhyloP100

0.93

Mutation Taster

=70/30

polymorphism

(source)

Splicing

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