rs2271205

Variant names:

• chr3-9037765-G-A
• rs2271205
• ENST00000485983.6:n.1343C>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 ENST00000485983.6(SRGAP3):​n.1343C>T variant causes a non coding transcript exon 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 ENST00000485983.6 non_coding_transcript_exon
• 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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRGAP3	NM_014850.4	c.1436+298C>T		intron_variant	Intron 11 of 21	ENST00000383836.8	NP_055665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRGAP3	ENST00000383836.8	c.1436+298C>T		intron_variant	Intron 11 of 21	1	NM_014850.4	ENSP00000373347.3

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 v4.3

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

Other links and lift over

dbSNP: rs2271205; hg19: chr3-9079449;