Genetic Variant MACC1-OT1:n.544-8513T>C (chr7-19939811-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000435968.5(MACC1-OT1):n.491-20551T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 152,036 control chromosomes in the GnomAD database, including 833 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 0.068 ( 833 hom., cov: 32)

Consequence

MACC1-OT1
ENST00000435968.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970

Publications

1 publications found

Variant links:

Genes affected

MACC1-OT1 (HGNC:58196):

MACC1-OT1 links:

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new If you want to explore the variant's impact on the transcript ENST00000435968.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435968.5. 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
	MACC1-OT1	NR_110114.1		n.543-20551T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MACC1-OT1	ENST00000415499.6	TSL:3	n.544-8513T>C	intron	N/A
MACC1-OT1	ENST00000435968.5	TSL:2	n.491-20551T>C	intron	N/A
MACC1-OT1	ENST00000437191.6	TSL:2	n.526-8513T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0679

AC:

10321

AN:

151918

Hom.:

826

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0228

Gnomad ASJ

AF:

0.0188

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.0891

Gnomad FIN

AF:

0.0211

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0126

Gnomad OTH

AF:

0.0431

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

GnomAD4 genome

AF:

0.0682

AC:

10365

AN:

152036

Hom.:

833

Cov.:

AF XY:

0.0692

AC XY:

5144

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.158

AC:

6529

AN:

41434

American (AMR)

AF:

0.0227

AC:

347

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0188

AC:

AN:

3462

East Asian (EAS)

AF:

0.351

AC:

1808

AN:

5150

South Asian (SAS)

AF:

0.0888

AC:

428

AN:

4820

European-Finnish (FIN)

AF:

0.0211

AC:

224

AN:

10596

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0126

AC:

855

AN:

67988

Other (OTH)

AF:

0.0460

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

431

862

1294

1725

2156

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0402

Hom.:

Bravo

AF:

0.0727

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.6

(source)

DANN

Benign

0.72

PhyloP100

-0.097

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over