rs35966925

Positions:

• chr3-9037442-C-CA
• chr3-9037442-C-CAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_014850.4(SRGAP3):​c.1436+620dupT variant causes a intron 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 NM_014850.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SRGAP3	NM_014850.4	c.1436+620dupT		intron_variant		ENST00000383836.8	NP_055665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRGAP3	ENST00000383836.8	c.1436+620dupT		intron_variant		1	NM_014850.4	ENSP00000373347.3

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25245 AN: 151984 Hom.: 2284 Cov.: 29

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.: 28 Cov.: 0 AF XY: 0.151 AC XY: 161 AN XY: 1068

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0877

Gnomad4 ASJ exome AF: 0.125

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.193

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.175

Gnomad4 OTH exome AF: 0.134

GnomAD4 genome AF: 0.166 AC: 25235 AN: 152102 Hom.: 2280 Cov.: 29 AF XY: 0.164 AC XY: 12220 AN XY: 74348

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.0379

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.176

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

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

LitVar

Other links and lift over

dbSNP: rs35966925; hg19: chr3-9079126;