3-9211314-C-T

Position:

• chr3-9211314-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000383836.8(SRGAP3):​c.67+37571G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,102 control chromosomes in the GnomAD database, including 2,483 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 (2483 hom., cov: 32)
• Consequence: SRGAP3 ENST00000383836.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRGAP3	NM_014850.4	c.67+37571G>A		intron_variant		ENST00000383836.8	NP_055665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRGAP3	ENST00000383836.8	c.67+37571G>A		intron_variant		1	NM_014850.4	ENSP00000373347	P1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25894 AN: 151984 Hom.: 2484 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.157

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.170 AC: 25907 AN: 152102 Hom.: 2483 Cov.: 32 AF XY: 0.172 AC XY: 12820 AN XY: 74354

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.156

Alfa AF: 0.159 Hom.: 2679

Bravo AF: 0.176

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.57

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: rs12638703; hg19: chr3-9252998;