rs2271205

Variant names:

• chr3-9037765-G-A
• rs2271205
• NM_014850.4:c.1436+298C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-9037765-G-A
• chr3-9037765-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014850.4(SRGAP3):​c.1436+298C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000286 in 349,074 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000029 (0 hom.)
• Consequence: SRGAP3 NM_014850.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550
• 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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+298C>T		intron	N/A	NP_055665.1	O43295-1
	SRGAP3	NM_001033117.3		c.1436+298C>T		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+298C>T		intron	N/A	ENSP00000373347.3	O43295-1
	SRGAP3	ENST00000360413.7	TSL:1	c.1436+298C>T		intron	N/A	ENSP00000353587.3	O43295-2
	SRGAP3	ENST00000485983.6	TSL:1	n.1343C>T		non_coding_transcript_exon	Exon 9 of 9

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000286 AC: 1 AN: 349074 Hom.: 0 Cov.: 2 AF XY: 0.00000543 AC XY: 1 AN XY: 184080

African (AFR) AF: 0.00 AC: 0 AN: 10228

American (AMR) AF: 0.00 AC: 0 AN: 14744

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10750

East Asian (EAS) AF: 0.00 AC: 0 AN: 23382

South Asian (SAS) AF: 0.00 AC: 0 AN: 40216

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20580

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1472

European-Non Finnish (NFE) AF: 0.00000482 AC: 1 AN: 207438

Other (OTH) AF: 0.00 AC: 0 AN: 20264

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.55

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2271205;

hg19: chr3-9079449;