dbSNP rs35966925: SRGAP3:n.1665dupT (chr3-9037442-C-CA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000485983.6(SRGAP3):n.1665dupT 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 0.166 in 154,164 control chromosomes in the GnomAD database, including 2,308 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2280 hom., cov: 29)

Exomes 𝑓: 0.15 ( 28 hom. )

Consequence

SRGAP3
ENST00000485983.6 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

1 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRGAP3	NM_014850.4 link	c.1436+620dupT		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+620dupT		intron_variant	Intron 11 of 21	1	NM_014850.4	ENSP00000373347.3		O43295-1

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25245

AN:

151984

Hom.:

2284

Cov.:

show subpopulations

Gnomad AFR

AF:

0.100

Gnomad AMI

AF:

0.0835

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.0380

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.178

GnomAD4 exome

AF:

0.150

AC:

309

AN:

2062

Hom.:

Cov.:

AF XY:

0.151

AC XY:

161

AN XY:

1068

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.0877

AC:

AN:

456

Ashkenazi Jewish (ASJ)

AF:

0.125

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.193

AC:

AN:

114

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.175

AC:

231

AN:

1318

Other (OTH)

AF:

0.134

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.166

AC:

25235

AN:

152102

Hom.:

2280

Cov.:

AF XY:

0.164

AC XY:

12220

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.100

AC:

4167

AN:

41524

American (AMR)

AF:

0.131

AC:

2001

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

593

AN:

3470

East Asian (EAS)

AF:

0.0379

AC:

196

AN:

5174

South Asian (SAS)

AF:

0.216

AC:

1039

AN:

4818

European-Finnish (FIN)

AF:

0.195

AC:

2055

AN:

10562

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.216

AC:

14672

AN:

67952

Other (OTH)

AF:

0.176

AC:

371

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1087

2175

3262

4350

5437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

292

584

876

1168

1460

<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:

0.183

Hom.:

322

Bravo

AF:

0.156

Asia WGS

AF:

0.103

AC:

360

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.1

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