NM_014850.4:c.1323+2765A>C

Variant names:

• chr3-9050262-T-G
• rs2662090
• NM_014850.4:c.1323+2765A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRGAP3	NM_014850.4	MANE Select	c.1323+2765A>C		intron	N/A	NP_055665.1
	SRGAP3	NM_001033117.3		c.1323+2765A>C		intron	N/A	NP_001028289.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRGAP3	ENST00000383836.8	TSL:1 MANE Select	c.1323+2765A>C		intron	N/A	ENSP00000373347.3
	SRGAP3	ENST00000360413.7	TSL:1	c.1323+2765A>C		intron	N/A	ENSP00000353587.3
	SRGAP3	ENST00000485983.6	TSL:1	n.932+2765A>C		intron	N/A

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

African (AFR) AF: 0.325 AC: 13486 AN: 41460

American (AMR) AF: 0.547 AC: 8358 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1599 AN: 3470

East Asian (EAS) AF: 0.659 AC: 3393 AN: 5146

South Asian (SAS) AF: 0.616 AC: 2966 AN: 4812

European-Finnish (FIN) AF: 0.554 AC: 5851 AN: 10556

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33169 AN: 67948

Other (OTH) AF: 0.488 AC: 1031 AN: 2112

Alfa AF: 0.485 Hom.: 79581

Bravo AF: 0.458

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.42
PhyloP100		0.22
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: rs2662090; hg19: chr3-9091946;