dbSNP rs2982510: SMAP2:c.237+82C>T (chr1-40406951-C-T) – 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.237+82C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 1,454,244 control chromosomes in the GnomAD database, including 47,405 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 0.30 ( 8105 hom., cov: 32)

Exomes 𝑓: 0.24 ( 39300 hom. )

Consequence

SMAP2
NM_022733.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.190

Publications

14 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:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMAP2	NM_022733.3 link	c.237+82C>T		intron_variant	Intron 2 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.237+82C>T		intron_variant	Intron 2 of 9	1	NM_022733.3	ENSP00000361803.3		Q8WU79-1

Frequencies

GnomAD3 genomes

AF:

0.304

AC:

46271

AN:

151996

Hom.:

8105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.485

Gnomad AMI

AF:

0.0835

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.293

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.238

Gnomad OTH

AF:

0.278

GnomAD4 exome

AF:

0.241

AC:

314133

AN:

1302130

Hom.:

39300

AF XY:

0.240

AC XY:

153991

AN XY:

641500

show subpopulations

African (AFR)

AF:

0.494

AC:

14318

AN:

28978

American (AMR)

AF:

0.241

AC:

7530

AN:

31256

Ashkenazi Jewish (ASJ)

AF:

0.215

AC:

4457

AN:

20718

East Asian (EAS)

AF:

0.273

AC:

9948

AN:

36416

South Asian (SAS)

AF:

0.228

AC:

15258

AN:

67060

European-Finnish (FIN)

AF:

0.198

AC:

9572

AN:

48242

Middle Eastern (MID)

AF:

0.213

AC:

916

AN:

4296

European-Non Finnish (NFE)

AF:

0.236

AC:

238922

AN:

1012030

Other (OTH)

AF:

0.249

AC:

13212

AN:

53134

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

11197

22394

33590

44787

55984

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.304

AC:

46287

AN:

152114

Hom.:

8105

Cov.:

AF XY:

0.299

AC XY:

22223

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.484

AC:

20088

AN:

41480

American (AMR)

AF:

0.261

AC:

3997

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

723

AN:

3470

East Asian (EAS)

AF:

0.292

AC:

1515

AN:

5188

South Asian (SAS)

AF:

0.228

AC:

1098

AN:

4822

European-Finnish (FIN)

AF:

0.187

AC:

1981

AN:

10576

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.238

AC:

16170

AN:

67970

Other (OTH)

AF:

0.274

AC:

580

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1541

3082

4623

6164

7705

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.258

Hom.:

23016

Bravo

AF:

0.315

Asia WGS

AF:

0.259

AC:

900

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.3

(source)

DANN

Benign

0.50

PhyloP100

0.19

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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rs2982510

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