Variant rs2982510 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.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

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=-0.82).

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/exons	MANE	Protein	UniProt
SMAP2	NM_022733.3 linkuse as main transcript	c.237+82C>T		intron_variant		ENST00000372718.8	NP_073570.1	Q8WU79-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMAP2	ENST00000372718.8 linkuse as main transcript	c.237+82C>T		intron_variant		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

Gnomad4 AFR exome

AF:

0.494

Gnomad4 AMR exome

AF:

0.241

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.273

Gnomad4 SAS exome

AF:

0.228

Gnomad4 FIN exome

AF:

0.198

Gnomad4 NFE exome

AF:

0.236

Gnomad4 OTH exome

AF:

0.249

GnomAD4 genome

AF:

0.304

AC:

46287

AN:

152114

Hom.:

8105

Cov.:

AF XY:

0.299

AC XY:

22223

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.484

Gnomad4 AMR

AF:

0.261

Gnomad4 ASJ

AF:

0.208

Gnomad4 EAS

AF:

0.292

Gnomad4 SAS

AF:

0.228

Gnomad4 FIN

AF:

0.187

Gnomad4 NFE

AF:

0.238

Gnomad4 OTH

AF:

0.274

Alfa

AF:

0.244

Hom.:

9938

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

DANN

Benign

0.50

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