rs11131157

Positions:

• chr3-9037251-G-A

Variant summary

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

The ENST00000383836.8(SRGAP3):​c.1436+812C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,136 control chromosomes in the GnomAD database, including 1,938 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 0.15 (1937 hom., cov: 33)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: SRGAP3 ENST00000383836.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

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=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRGAP3	NM_014850.4	c.1436+812C>T		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+812C>T		intron_variant		1	NM_014850.4	ENSP00000373347	P1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22899 AN: 151994 Hom.: 1939 Cov.: 33

Gnomad AFR AF: 0.0810

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0355

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.164

GnomAD4 exome AF: 0.333 AC: 8 AN: 24 Hom.: 1 Cov.: 0 AF XY: 0.278 AC XY: 5 AN XY: 18

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.313

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.151 AC: 22895 AN: 152112 Hom.: 1937 Cov.: 33 AF XY: 0.149 AC XY: 11074 AN XY: 74356

Gnomad4 AFR AF: 0.0811

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0354

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.161

Alfa AF: 0.174 Hom.: 519

Bravo AF: 0.141

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.8
DANN	Benign	0.81

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: rs11131157; hg19: chr3-9078935;