dbSNP rs2294752: 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022733.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SMAP2	NM_022733.3	MANE Select	c.571+40T>G	intron	N/A	NP_073570.1	Q8WU79-1
SMAP2	NM_001198979.2		c.556+40T>G	intron	N/A	NP_001185908.1	A0A087WV97
SMAP2	NM_001198978.2		c.481+40T>G	intron	N/A	NP_001185907.1	Q8WU79-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SMAP2	ENST00000372718.8	TSL:1 MANE Select	c.571+40T>G	intron	N/A	ENSP00000361803.3	Q8WU79-1
SMAP2	ENST00000614549.4	TSL:1	c.556+40T>G	intron	N/A	ENSP00000479285.1	A0A087WV97
SMAP2	ENST00000372708.5	TSL:1	c.481+40T>G	intron	N/A	ENSP00000361793.1	Q8WU79-2

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over