Genetic Variant SMAP2:c.571+40T>G (chr1-40414280-T-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_022733.3(SMAP2):c.571+40T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 1,588,576 control chromosomes in the GnomAD database, including 51,936 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 0.31 ( 8201 hom., cov: 32)

Exomes 𝑓: 0.24 ( 43735 hom. )

Consequence

SMAP2
NM_022733.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.463

Publications

10 publications found

Variant links:

Genes affected

SMAP2 (HGNC:25082): (small ArfGAP2) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of catalytic activity. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SMAP2 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=-0.57).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMAP2	NM_022733.3 link	c.571+40T>G		intron_variant	Intron 6 of 9	ENST00000372718.8	NP_073570.1	Q8WU79-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMAP2	ENST00000372718.8 link	c.571+40T>G		intron_variant	Intron 6 of 9	1	NM_022733.3	ENSP00000361803.3		Q8WU79-1

Frequencies

GnomAD3 genomes

AF:

0.306

AC:

46474

AN:

152004

Hom.:

8199

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.0835

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.294

Gnomad SAS

AF:

0.230

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.238

Gnomad OTH

AF:

0.279

GnomAD2 exomes

AF:

0.252

AC:

62178

AN:

246906

AF XY:

0.247

show subpopulations

Gnomad AFR exome

AF:

0.489

Gnomad AMR exome

AF:

0.242

Gnomad ASJ exome

AF:

0.219

Gnomad EAS exome

AF:

0.293

Gnomad FIN exome

AF:

0.189

Gnomad NFE exome

AF:

0.233

Gnomad OTH exome

AF:

0.255

GnomAD4 exome

AF:

0.243

AC:

349146

AN:

1436454

Hom.:

43735

Cov.:

AF XY:

0.242

AC XY:

173276

AN XY:

716084

show subpopulations

African (AFR)

AF:

0.497

AC:

16335

AN:

32880

American (AMR)

AF:

0.244

AC:

10792

AN:

44294

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

5638

AN:

25938

East Asian (EAS)

AF:

0.276

AC:

10912

AN:

39550

South Asian (SAS)

AF:

0.234

AC:

19994

AN:

85434

European-Finnish (FIN)

AF:

0.199

AC:

10596

AN:

53270

Middle Eastern (MID)

AF:

0.212

AC:

1212

AN:

5718

European-Non Finnish (NFE)

AF:

0.237

AC:

258728

AN:

1089834

Other (OTH)

AF:

0.251

AC:

14939

AN:

59536

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

13009

26018

39026

52035

65044

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9000

18000

27000

36000

45000

<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:

0.306

AC:

46496

AN:

152122

Hom.:

8201

Cov.:

AF XY:

0.300

AC XY:

22326

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.488

AC:

20257

AN:

41476

American (AMR)

AF:

0.262

AC:

4003

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

723

AN:

3472

East Asian (EAS)

AF:

0.293

AC:

1519

AN:

5182

South Asian (SAS)

AF:

0.229

AC:

1103

AN:

4822

European-Finnish (FIN)

AF:

0.187

AC:

1979

AN:

10588

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.238

AC:

16197

AN:

67986

Other (OTH)

AF:

0.275

AC:

580

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1583

3167

4750

6334

7917

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

444

888

1332

1776

2220

<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:

0.263

Hom.:

2523

Bravo

AF:

0.316

Asia WGS

AF:

0.260

AC:

904

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

5.9

(source)

DANN

Benign

0.87

PhyloP100

-0.46

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over