Genetic Variant SRGAP3:n.1343C>G (chr3-9037765-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000485983.6(SRGAP3):n.1343C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 500,372 control chromosomes in the GnomAD database, including 16,455 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 0.24 ( 4452 hom., cov: 33)

Exomes 𝑓: 0.26 ( 12003 hom. )

Consequence

SRGAP3
ENST00000485983.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.550

Publications

0 publications found

Variant links:

Genes affected

SRGAP3 (HGNC:19744): (SLIT-ROBO Rho GTPase activating protein 3) Predicted to enable GTPase activator activity. Predicted to be involved in negative regulation of cell migration. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SRGAP3 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRGAP3	NM_014850.4 link	c.1436+298C>G		intron_variant	Intron 11 of 21	ENST00000383836.8	NP_055665.1	O43295-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRGAP3	ENST00000383836.8 link	c.1436+298C>G		intron_variant	Intron 11 of 21	1	NM_014850.4	ENSP00000373347.3		O43295-1

Frequencies

GnomAD3 genomes

AF:

0.241

AC:

36632

AN:

152018

Hom.:

4451

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.243

GnomAD4 exome

AF:

0.256

AC:

89271

AN:

348236

Hom.:

12003

Cov.:

AF XY:

0.262

AC XY:

48121

AN XY:

183632

show subpopulations

African (AFR)

AF:

0.222

AC:

2266

AN:

10208

American (AMR)

AF:

0.142

AC:

2093

AN:

14714

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

2352

AN:

10728

East Asian (EAS)

AF:

0.136

AC:

3178

AN:

23348

South Asian (SAS)

AF:

0.336

AC:

13483

AN:

40102

European-Finnish (FIN)

AF:

0.252

AC:

5181

AN:

20528

Middle Eastern (MID)

AF:

0.293

AC:

430

AN:

1470

European-Non Finnish (NFE)

AF:

0.267

AC:

55196

AN:

206904

Other (OTH)

AF:

0.252

AC:

5092

AN:

20234

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3064

6127

9191

12254

15318

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

306

612

918

1224

1530

<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:

0.241

AC:

36646

AN:

152136

Hom.:

4452

Cov.:

AF XY:

0.239

AC XY:

17795

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.222

AC:

9230

AN:

41514

American (AMR)

AF:

0.173

AC:

2640

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

777

AN:

3472

East Asian (EAS)

AF:

0.127

AC:

656

AN:

5168

South Asian (SAS)

AF:

0.324

AC:

1561

AN:

4818

European-Finnish (FIN)

AF:

0.254

AC:

2690

AN:

10588

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.271

AC:

18391

AN:

67964

Other (OTH)

AF:

0.240

AC:

507

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1466

2932

4397

5863

7329

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.251

Hom.:

624

Bravo

AF:

0.230

Asia WGS

AF:

0.199

AC:

693

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.1

(source)

DANN

Benign

0.45

PhyloP100

-0.55

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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