Genetic Variant MANEA-DT:n.64+4136T>A (chr6-95573494-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000791249.1(MANEA-DT):n.64+4136T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,882 control chromosomes in the GnomAD database, including 28,110 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 0.60 ( 28110 hom., cov: 31)

Consequence

MANEA-DT
ENST00000791249.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Publications

6 publications found

Variant links:

Genes affected

MANEA-DT (HGNC:43732): (MANEA divergent transcript)

MANEA-DT 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MANEA-DT	NR_104136.1 link	n.359+3599T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MANEA-DT	ENST00000791249.1 link	n.64+4136T>A	intron_variant	Intron 1 of 3
MANEA-DT	ENST00000791250.1 link	n.354+3599T>A	intron_variant	Intron 1 of 2
MANEA-DT	ENST00000791251.1 link	n.357+3599T>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.604

AC:

91637

AN:

151764

Hom.:

28098

Cov.:

show subpopulations

Gnomad AFR

AF:

0.643

Gnomad AMI

AF:

0.528

Gnomad AMR

AF:

0.537

Gnomad ASJ

AF:

0.596

Gnomad EAS

AF:

0.870

Gnomad SAS

AF:

0.738

Gnomad FIN

AF:

0.530

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.577

Gnomad OTH

AF:

0.623

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

GnomAD4 genome

AF:

0.604

AC:

91688

AN:

151882

Hom.:

28110

Cov.:

AF XY:

0.602

AC XY:

44672

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.642

AC:

26594

AN:

41404

American (AMR)

AF:

0.537

AC:

8190

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.596

AC:

2066

AN:

3468

East Asian (EAS)

AF:

0.870

AC:

4487

AN:

5156

South Asian (SAS)

AF:

0.737

AC:

3550

AN:

4818

European-Finnish (FIN)

AF:

0.530

AC:

5595

AN:

10562

Middle Eastern (MID)

AF:

0.707

AC:

208

AN:

294

European-Non Finnish (NFE)

AF:

0.577

AC:

39197

AN:

67898

Other (OTH)

AF:

0.626

AC:

1324

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1847

3694

5542

7389

9236

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

774

1548

2322

3096

3870

<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:

0.444

Hom.:

1188

Bravo

AF:

0.604

Asia WGS

AF:

0.779

AC:

2707

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.18

(source)

DANN

Benign

0.49

PhyloP100

-1.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over