3-9343030-T-C

Variant names:

• chr3-9343030-T-C
• rs2600197
• ENST00000490889.2:n.215-12434A>G

Variant summary

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

The ENST00000490889.2(SRGAP3):​n.215-12434A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,202 control chromosomes in the GnomAD database, including 50,864 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 0.81 (50864 hom., cov: 32)
• Consequence: SRGAP3 ENST00000490889.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 0 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]

ENSG00000254485 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRGAP3	XM_024453843.2	c.-521-12434A>G		intron_variant	Intron 1 of 24		XP_024309611.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRGAP3	ENST00000490889.2	n.215-12434A>G		intron_variant	Intron 1 of 3	4
ENSG00000254485	ENST00000491930.2	n.191-16862A>G		intron_variant	Intron 1 of 3	3
ENSG00000254485	ENST00000518331.1	n.465-5353A>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123534 AN: 152084 Hom.: 50816 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.812 AC: 123639 AN: 152202 Hom.: 50864 Cov.: 32 AF XY: 0.818 AC XY: 60864 AN XY: 74416

African (AFR) AF: 0.926 AC: 38476 AN: 41542

American (AMR) AF: 0.834 AC: 12758 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2661 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4803 AN: 5180

South Asian (SAS) AF: 0.900 AC: 4335 AN: 4814

European-Finnish (FIN) AF: 0.747 AC: 7910 AN: 10586

Middle Eastern (MID) AF: 0.812 AC: 237 AN: 292

European-Non Finnish (NFE) AF: 0.736 AC: 50076 AN: 67998

Other (OTH) AF: 0.811 AC: 1716 AN: 2116

Alfa AF: 0.702 Hom.: 2315

Bravo AF: 0.822

Asia WGS AF: 0.903 AC: 3141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2600197; hg19: chr3-9384714;