rs2483058

Variant names:

• chr1-206453482-G-C
• rs2483058
• NM_015326.5:c.2360+102G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-206453482-G-C
• chr1-206453482-G-T

Variant summary

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

The NM_015326.5(SRGAP2):​c.2360+102G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 468,832 control chromosomes in the GnomAD database, including 55,507 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 0.51 (20582 hom., cov: 29)
  • Exomes 𝑓: 0.45 (34925 hom.)
• Consequence: SRGAP2 NM_015326.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445
• Publications: 12 publications found

Genes affected

SRGAP2 (HGNC:19751): (SLIT-ROBO Rho GTPase activating protein 2) This locus encodes a member of the SLIT-ROBO Rho GTPase activating protein family. The encoded protein stimulates GTPase activity of Rac1, and plays a role in cortical neuron development. This locus has several paralogs on human chromosome 1 resulting from segmental duplication. While this locus itself is conserved among various species, the paralogs are found only in the genus Homo, and not in the genomes of non-human great apes. Alternatively spliced transcript variants have been described for this locus. [provided by RefSeq, Jul 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015326.5. 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
	SRGAP2	NM_015326.5	MANE Select	c.2360+102G>C		intron	N/A	NP_056141.2
	SRGAP2	NM_001170637.4		c.2357+102G>C		intron	N/A	NP_001164108.1
	SRGAP2	NM_001377444.1		c.2360+102G>C		intron	N/A	NP_001364373.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRGAP2	ENST00000573034.8	TSL:1 MANE Select	c.2360+102G>C		intron	N/A	ENSP00000459615.2
	SRGAP2	ENST00000624873.3	TSL:1	c.2357+102G>C		intron	N/A	ENSP00000485517.1
	SRGAP2	ENST00000605476.5	TSL:1	c.1202+102G>C		intron	N/A	ENSP00000474270.1

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76559 AN: 151106 Hom.: 20543 Cov.: 29

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.468

GnomAD4 exome AF: 0.452 AC: 143603 AN: 317608 Hom.: 34925 Cov.: 0 AF XY: 0.450 AC XY: 74423 AN XY: 165448

African (AFR) AF: 0.659 AC: 5017 AN: 7608

American (AMR) AF: 0.503 AC: 4598 AN: 9142

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 4015 AN: 10180

East Asian (EAS) AF: 0.773 AC: 18036 AN: 23336

South Asian (SAS) AF: 0.518 AC: 10286 AN: 19844

European-Finnish (FIN) AF: 0.507 AC: 20276 AN: 39984

Middle Eastern (MID) AF: 0.383 AC: 691 AN: 1806

European-Non Finnish (NFE) AF: 0.386 AC: 72100 AN: 186844

Other (OTH) AF: 0.455 AC: 8584 AN: 18864

GnomAD4 genome AF: 0.507 AC: 76660 AN: 151224 Hom.: 20582 Cov.: 29 AF XY: 0.514 AC XY: 37954 AN XY: 73800

African (AFR) AF: 0.665 AC: 27341 AN: 41120

American (AMR) AF: 0.496 AC: 7540 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1428 AN: 3462

East Asian (EAS) AF: 0.729 AC: 3693 AN: 5068

South Asian (SAS) AF: 0.586 AC: 2807 AN: 4794

European-Finnish (FIN) AF: 0.503 AC: 5217 AN: 10378

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27059 AN: 67882

Other (OTH) AF: 0.474 AC: 995 AN: 2100

Alfa AF: 0.279 Hom.: 601

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
PhyloP100		0.45
PromoterAI		-0.0032	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2483058; hg19: chr1-206626828;