rs2662090

chr3-9050262-T-G

Variant summary

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

The NM_014850.4(SRGAP3):c.1323+2765A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,978 control chromosomes in the GnomAD database, including 17,193 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 0.46 (17193 hom., cov: 32)
• Consequence: SRGAP3 NM_014850.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRGAP3	NM_014850.4	c.1323+2765A>C		intron_variant		ENST00000383836.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRGAP3	ENST00000383836.8	c.1323+2765A>C		intron_variant		1	NM_014850.4	P1
SRGAP3	ENST00000360413.7	c.1323+2765A>C		intron_variant		1
SRGAP3	ENST00000485983.6	n.932+2765A>C		intron_variant, non_coding_transcript_variant		1
SRGAP3	ENST00000433332.7	n.1393-793A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70500 AN: 151860 Hom.: 17176 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.464 AC: 70551 AN: 151978 Hom.: 17193 Cov.: 32 AF XY: 0.473 AC XY: 35121 AN XY: 74266

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.488

Alfa AF: 0.490 Hom.: 37561

Bravo AF: 0.458

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.3
Dann	Benign	0.42

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: rs2662090; hg19: chr3-9091946;