dbSNP rs3134615: MYCL:c.*978G>T (chr1-39896394-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001033081.3(MYCL):c.*978G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 203,210 control chromosomes in the GnomAD database, including 3,666 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 0.17 ( 2597 hom., cov: 32)

Exomes 𝑓: 0.19 ( 1069 hom. )

Consequence

MYCL
NM_001033081.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.184

Publications

38 publications found

Variant links:

Genes affected

MYCL (HGNC:7555): (MYCL proto-oncogene, bHLH transcription factor) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of inner ear auditory receptor cell differentiation. Located in chromosome and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MYCL links:

MYCL-AS1 (HGNC:40386): (MYCL antisense RNA 1)

MYCL-AS1 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=-0.64).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001033081.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYCL	NM_001033081.3	MANE Select	c.*978G>T	3_prime_UTR	Exon 2 of 2	NP_001028253.1	P12524-1
MYCL	NM_001033082.3		c.*978G>T	3_prime_UTR	Exon 3 of 3	NP_001028254.2	P12524-3
MYCL-AS1	NR_183424.1		n.273-1349C>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYCL	ENST00000372816.3	TSL:2 MANE Select	c.*978G>T	3_prime_UTR	Exon 2 of 2	ENSP00000361903.2	P12524-1
MYCL	ENST00000397332.3	TSL:1	c.*978G>T	3_prime_UTR	Exon 3 of 3	ENSP00000380494.2	P12524-3
MYCL-AS1	ENST00000418255.2	TSL:2	n.326-1349C>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26348

AN:

152070

Hom.:

2600

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0901

Gnomad AMI

AF:

0.0910

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.0374

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.180

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.163

GnomAD4 exome

AF:

0.187

AC:

9557

AN:

51022

Hom.:

1069

Cov.:

AF XY:

0.192

AC XY:

4548

AN XY:

23724

show subpopulations

African (AFR)

AF:

0.0923

AC:

202

AN:

2188

American (AMR)

AF:

0.149

AC:

215

AN:

1444

Ashkenazi Jewish (ASJ)

AF:

0.271

AC:

872

AN:

3212

East Asian (EAS)

AF:

0.0229

AC:

189

AN:

8242

South Asian (SAS)

AF:

0.211

AC:

AN:

426

European-Finnish (FIN)

AF:

0.220

AC:

AN:

Middle Eastern (MID)

AF:

0.138

AC:

AN:

298

European-Non Finnish (NFE)

AF:

0.230

AC:

7109

AN:

30910

Other (OTH)

AF:

0.195

AC:

821

AN:

4220

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

370

740

1110

1480

1850

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.173

AC:

26346

AN:

152188

Hom.:

2597

Cov.:

AF XY:

0.170

AC XY:

12682

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.0900

AC:

3740

AN:

41538

American (AMR)

AF:

0.143

AC:

2180

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

857

AN:

3470

East Asian (EAS)

AF:

0.0375

AC:

194

AN:

5178

South Asian (SAS)

AF:

0.217

AC:

1046

AN:

4824

European-Finnish (FIN)

AF:

0.180

AC:

1901

AN:

10580

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.235

AC:

15963

AN:

67990

Other (OTH)

AF:

0.161

AC:

341

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1106

2213

3319

4426

5532

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

292

584

876

1168

1460

<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:

0.216

Hom.:

6659

Bravo

AF:

0.165

Asia WGS

AF:

0.129

AC:

450

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

6.0

(source)

DANN

Benign

0.59

PhyloP100

0.18

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over