Genetic Variant SRGAP3:n.1664C>T (chr3-9037444-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000485983.6(SRGAP3):n.1664C>T 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 154,226 control chromosomes in the GnomAD database, including 2,310 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 0.17 ( 2282 hom., cov: 33)

Exomes 𝑓: 0.15 ( 28 hom. )

Consequence

SRGAP3
ENST00000485983.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.558

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000485983.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRGAP3	NM_014850.4	MANE Select	c.1436+619C>T		intron	N/A	NP_055665.1
	SRGAP3	NM_001033117.3		c.1436+619C>T		intron	N/A	NP_001028289.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SRGAP3	ENST00000485983.6	TSL:1	n.1664C>T	non_coding_transcript_exon	Exon 9 of 9
SRGAP3	ENST00000383836.8	TSL:1 MANE Select	c.1436+619C>T	intron	N/A	ENSP00000373347.3
SRGAP3	ENST00000360413.7	TSL:1	c.1436+619C>T	intron	N/A	ENSP00000353587.3

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25251

AN:

152004

Hom.:

2286

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:

0.0382

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.194

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.178

GnomAD4 exome

AF:

0.147

AC:

309

AN:

2104

Hom.:

Cov.:

AF XY:

0.147

AC XY:

160

AN XY:

1088

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.0881

AC:

AN:

454

Ashkenazi Jewish (ASJ)

AF:

0.100

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.183

AC:

AN:

120

European-Finnish (FIN)

AF:

0.192

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.171

AC:

230

AN:

1344

Other (OTH)

AF:

0.128

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

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:

25241

AN:

152122

Hom.:

2282

Cov.:

AF XY:

0.164

AC XY:

12223

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.100

AC:

4167

AN:

41532

American (AMR)

AF:

0.131

AC:

2004

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

593

AN:

3470

East Asian (EAS)

AF:

0.0380

AC:

197

AN:

5178

South Asian (SAS)

AF:

0.216

AC:

1039

AN:

4816

European-Finnish (FIN)

AF:

0.194

AC:

2055

AN:

10572

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.216

AC:

14674

AN:

67956

Other (OTH)

AF:

0.176

AC:

371

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1072

2144

3217

4289

5361

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:

0.164

Hom.:

1096

Bravo

AF:

0.156

Asia WGS

AF:

0.103

AC:

360

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

0.56

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over