Variant chr1-40414280-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SMAP2	NM_022733.3 linkuse as main transcript	c.571+40T>G		intron_variant		ENST00000372718.8	NP_073570.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMAP2	ENST00000372718.8 linkuse as main transcript	c.571+40T>G		intron_variant		1	NM_022733.3	ENSP00000361803	P1	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

GnomAD3 exomes

AF:

0.252

AC:

62178

AN:

246906

Hom.:

8260

AF XY:

0.247

AC XY:

33007

AN XY:

133530

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 SAS exome

AF:

0.234

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

Gnomad4 AFR exome

AF:

0.497

Gnomad4 AMR exome

AF:

0.244

Gnomad4 ASJ exome

AF:

0.217

Gnomad4 EAS exome

AF:

0.276

Gnomad4 SAS exome

AF:

0.234

Gnomad4 FIN exome

AF:

0.199

Gnomad4 NFE exome

AF:

0.237

Gnomad4 OTH exome

AF:

0.251

GnomAD4 genome

AF:

0.306

AC:

46496

AN:

152122

Hom.:

8201

Cov.:

AF XY:

0.300

AC XY:

22326

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.488

Gnomad4 AMR

AF:

0.262

Gnomad4 ASJ

AF:

0.208

Gnomad4 EAS

AF:

0.293

Gnomad4 SAS

AF:

0.229

Gnomad4 FIN

AF:

0.187

Gnomad4 NFE

AF:

0.238

Gnomad4 OTH

AF:

0.275

Alfa

AF:

0.261

Hom.:

1711

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

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

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