Genetic Variant NM_015251.3:c.336+886A>G (chr16-81037092-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015251.3(ATMIN):c.336+886A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 778,564 control chromosomes in the GnomAD database, including 280,940 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 0.74 ( 44581 hom., cov: 31)

Exomes 𝑓: 0.87 ( 236359 hom. )

Consequence

ATMIN
NM_015251.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0480

Publications

19 publications found

Variant links:

Genes affected

ATMIN (HGNC:29034): (ATM interactor) Enables dynein complex binding activity. Involved in positive regulation of transcription, DNA-templated. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ATMIN links:

ENSG00000284512 (HGNC:):

ENSG00000284512 links:

CENPN-AS1 (HGNC:55106): (CENPN antisense RNA 1)

CENPN-AS1 links:

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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=-0.71).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015251.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATMIN	NM_015251.3	MANE Select	c.336+886A>G		intron	N/A	NP_056066.2
	ATMIN	NM_001300728.2		c.-516A>G		upstream_gene	N/A	NP_001287657.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ATMIN	ENST00000299575.5	TSL:1 MANE Select	c.336+886A>G	intron	N/A	ENSP00000299575.3
ENSG00000284512	ENST00000640345.1	TSL:5	c.425-2166T>C	intron	N/A	ENSP00000492798.1
ENSG00000284512	ENST00000638192.1	TSL:5	c.131-2166T>C	intron	N/A	ENSP00000492056.1

Frequencies

GnomAD3 genomes

AF:

0.745

AC:

113151

AN:

151938

Hom.:

44574

Cov.:

show subpopulations

Gnomad AFR

AF:

0.453

Gnomad AMI

AF:

0.971

Gnomad AMR

AF:

0.813

Gnomad ASJ

AF:

0.896

Gnomad EAS

AF:

0.729

Gnomad SAS

AF:

0.869

Gnomad FIN

AF:

0.794

Gnomad MID

AF:

0.877

Gnomad NFE

AF:

0.878

Gnomad OTH

AF:

0.796

GnomAD4 exome

AF:

0.866

AC:

542449

AN:

626508

Hom.:

236359

AF XY:

0.867

AC XY:

253951

AN XY:

292944

show subpopulations

African (AFR)

AF:

0.415

AC:

4814

AN:

11598

American (AMR)

AF:

0.858

AC:

604

AN:

704

Ashkenazi Jewish (ASJ)

AF:

0.906

AC:

3505

AN:

3870

East Asian (EAS)

AF:

0.729

AC:

1952

AN:

2678

South Asian (SAS)

AF:

0.880

AC:

10741

AN:

12200

European-Finnish (FIN)

AF:

0.821

AC:

174

AN:

212

Middle Eastern (MID)

AF:

0.875

AC:

1095

AN:

1252

European-Non Finnish (NFE)

AF:

0.876

AC:

502127

AN:

573402

Other (OTH)

AF:

0.847

AC:

17437

AN:

20592

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

3236

6471

9707

12942

16178

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14934

29868

44802

59736

74670

<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:

0.744

AC:

113183

AN:

152056

Hom.:

44581

Cov.:

AF XY:

0.744

AC XY:

55330

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.453

AC:

18746

AN:

41422

American (AMR)

AF:

0.813

AC:

12427

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.896

AC:

3110

AN:

3472

East Asian (EAS)

AF:

0.730

AC:

3779

AN:

5176

South Asian (SAS)

AF:

0.871

AC:

4197

AN:

4820

European-Finnish (FIN)

AF:

0.794

AC:

8389

AN:

10568

Middle Eastern (MID)

AF:

0.874

AC:

257

AN:

294

European-Non Finnish (NFE)

AF:

0.878

AC:

59713

AN:

68004

Other (OTH)

AF:

0.795

AC:

1679

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1225

2450

3676

4901

6126

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

834

1668

2502

3336

4170

<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:

0.838

Hom.:

209386

Bravo

AF:

0.729

Asia WGS

AF:

0.789

AC:

2743

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

(source)

DANN

Benign

0.88

PhyloP100

-0.048

PromoterAI

0.063

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over