3-9211314-C-T

Variant names:

• chr3-9211314-C-T
• rs12638703
• NM_014850.4:c.67+37571G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014850.4(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 NM_014850.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014850.4. 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.67+37571G>A		intron	N/A	NP_055665.1
	SRGAP3	NM_001033117.3		c.67+37571G>A		intron	N/A	NP_001028289.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRGAP3	ENST00000383836.8	TSL:1 MANE Select	c.67+37571G>A		intron	N/A	ENSP00000373347.3
	SRGAP3	ENST00000360413.7	TSL:1	c.67+37571G>A		intron	N/A	ENSP00000353587.3
	SRGAP3	ENST00000433332.7	TSL:5	n.136+5311G>A		intron	N/A

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

African (AFR) AF: 0.166 AC: 6874 AN: 41480

American (AMR) AF: 0.180 AC: 2747 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2541 AN: 5170

South Asian (SAS) AF: 0.159 AC: 768 AN: 4822

European-Finnish (FIN) AF: 0.142 AC: 1503 AN: 10578

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10557 AN: 67980

Other (OTH) AF: 0.156 AC: 329 AN: 2112

Alfa AF: 0.166 Hom.: 7371

Bravo AF: 0.176

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.57
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12638703; hg19: chr3-9252998;