Variant chr16-81043216-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015251.3(ATMIN):c.718T>C(p.Ser240Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0861 in 1,613,118 control chromosomes in the GnomAD database, including 6,793 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.079 ( 529 hom., cov: 32)

Exomes 𝑓: 0.087 ( 6264 hom. )

Consequence

ATMIN
NM_015251.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.27

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.6076727E-4).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATMIN	NM_015251.3 linkuse as main transcript	c.718T>C	p.Ser240Pro	missense_variant	4/4	ENST00000299575.5
ATMIN	NM_001300728.2 linkuse as main transcript	c.250T>C	p.Ser84Pro	missense_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATMIN	ENST00000299575.5 linkuse as main transcript	c.718T>C	p.Ser240Pro	missense_variant	4/4	1	NM_015251.3	P1	O43313-1
ATMIN	ENST00000564241.5 linkuse as main transcript	c.250T>C	p.Ser84Pro	missense_variant	4/4	1			O43313-2
ATMIN	ENST00000566488.1 linkuse as main transcript	c.250T>C	p.Ser84Pro	missense_variant	3/3	1			O43313-2
ATMIN	ENST00000539819.5 linkuse as main transcript	n.476T>C		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.0790

AC:

12015

AN:

152038

Hom.:

528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0454

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.0522

Gnomad EAS

AF:

0.201

Gnomad SAS

AF:

0.0816

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0799

Gnomad OTH

AF:

0.0727

GnomAD3 exomes

AF:

0.100

AC:

25109

AN:

250652

Hom.:

1575

AF XY:

0.0958

AC XY:

12982

AN XY:

135498

show subpopulations

Gnomad AFR exome

AF:

0.0499

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.0552

Gnomad EAS exome

AF:

0.213

Gnomad SAS exome

AF:

0.0730

Gnomad FIN exome

AF:

0.122

Gnomad NFE exome

AF:

0.0795

Gnomad OTH exome

AF:

0.0868

GnomAD4 exome

AF:

0.0868

AC:

126833

AN:

1460960

Hom.:

6264

Cov.:

AF XY:

0.0855

AC XY:

62132

AN XY:

726792

show subpopulations

Gnomad4 AFR exome

AF:

0.0442

Gnomad4 AMR exome

AF:

0.151

Gnomad4 ASJ exome

AF:

0.0551

Gnomad4 EAS exome

AF:

0.202

Gnomad4 SAS exome

AF:

0.0709

Gnomad4 FIN exome

AF:

0.121

Gnomad4 NFE exome

AF:

0.0821

Gnomad4 OTH exome

AF:

0.0850

GnomAD4 genome

AF:

0.0790

AC:

12018

AN:

152158

Hom.:

529

Cov.:

AF XY:

0.0814

AC XY:

6055

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.0455

Gnomad4 AMR

AF:

0.106

Gnomad4 ASJ

AF:

0.0522

Gnomad4 EAS

AF:

0.200

Gnomad4 SAS

AF:

0.0800

Gnomad4 FIN

AF:

0.121

Gnomad4 NFE

AF:

0.0799

Gnomad4 OTH

AF:

0.0747

Alfa

AF:

0.0751

Hom.:

369

Bravo

AF:

0.0797

TwinsUK

AF:

0.0898

AC:

333

ALSPAC

AF:

0.0804

AC:

310

ESP6500AA

AF:

0.0495

AC:

218

ESP6500EA

AF:

0.0737

AC:

634

ExAC

AF:

0.0974

AC:

11830

Asia WGS

AF:

0.130

AC:

453

AN:

3478

EpiCase

AF:

0.0736

EpiControl

AF:

0.0739

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.078

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.25

T;.;.

Eigen

Benign

-0.44

Eigen_PC

Benign

-0.41

FATHMM_MKL

Uncertain

0.79

LIST_S2

Benign

0.67

T;.;T

MetaRNN

Benign

0.00096

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.7

M;.;.

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.43

PROVEAN

Benign

-0.98

N;.;N

REVEL

Benign

0.046

Sift

Uncertain

0.0020

D;.;D

Sift4G

Uncertain

0.031

D;T;T

Polyphen

0.0030

B;.;.

Vest4

0.066

MPC

0.033

ClinPred

0.031

GERP RS

3.7

Varity_R

0.19

gMVP

0.70

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over