rs35966925

Variant names:

• chr3-9037442-C-CA
• rs35966925
• NM_014850.4:c.1436+620dupT

Your query was ambiguous. Multiple possible variants found:

• chr3-9037442-C-CA
• chr3-9037442-C-CAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_014850.4(SRGAP3):​c.1436+620dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 154,164 control chromosomes in the GnomAD database, including 2,308 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.17 (2280 hom., cov: 29)
  • Exomes 𝑓: 0.15 (28 hom.)
• Consequence: SRGAP3 NM_014850.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 1 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 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.1436+620dupT		intron	N/A	NP_055665.1	O43295-1
	SRGAP3	NM_001033117.3		c.1436+620dupT		intron	N/A	NP_001028289.1	O43295-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRGAP3	ENST00000383836.8	TSL:1 MANE Select	c.1436+620dupT		intron	N/A	ENSP00000373347.3	O43295-1
	SRGAP3	ENST00000360413.7	TSL:1	c.1436+620dupT		intron	N/A	ENSP00000353587.3	O43295-2
	SRGAP3	ENST00000485983.6	TSL:1	n.1665dupT		non_coding_transcript_exon	Exon 9 of 9

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25245 AN: 151984 Hom.: 2284 Cov.: 29

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0380

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.178

GnomAD4 exome AF: 0.150 AC: 309 AN: 2062 Hom.: 28 Cov.: 0 AF XY: 0.151 AC XY: 161 AN XY: 1068

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.0877 AC: 40 AN: 456

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 1 AN: 8

East Asian (EAS) AF: 0.00 AC: 0 AN: 48

South Asian (SAS) AF: 0.193 AC: 22 AN: 114

European-Finnish (FIN) AF: 0.167 AC: 4 AN: 24

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.175 AC: 231 AN: 1318

Other (OTH) AF: 0.134 AC: 11 AN: 82

GnomAD4 genome AF: 0.166 AC: 25235 AN: 152102 Hom.: 2280 Cov.: 29 AF XY: 0.164 AC XY: 12220 AN XY: 74348

African (AFR) AF: 0.100 AC: 4167 AN: 41524

American (AMR) AF: 0.131 AC: 2001 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3470

East Asian (EAS) AF: 0.0379 AC: 196 AN: 5174

South Asian (SAS) AF: 0.216 AC: 1039 AN: 4818

European-Finnish (FIN) AF: 0.195 AC: 2055 AN: 10562

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14672 AN: 67952

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.183 Hom.: 322

Bravo AF: 0.156

Asia WGS AF: 0.103 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1
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: rs35966925; hg19: chr3-9079126;