1-121370191-C-T

Variant names:

• chr1-121370191-C-T
• rs2580520
• NM_001329984.2:c.487-3780C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001329984.2(SRGAP2C):​c.487-3780C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 7)
• Consequence: SRGAP2C NM_001329984.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 6 publications found

Genes affected

SRGAP2C (HGNC:30584): (SLIT-ROBO Rho GTPase activating protein 2C) This locus encodes a member of the SLIT-ROBO Rho GTPase activating protein family. This human-specific locus resulted from segmental duplication of the SLIT-ROBO Rho GTPase activating protein 2B locus. The encoded protein lacks the GTPase activating protein domain compared to proteins encoded by SLIT-ROBO Rho GTPase activating protein 2, and acts antagonistically to these proteins in cortical neuron development. [provided by RefSeq, Dec 2012]

SRGAP2-AS1 (HGNC:40902): (SRGAP2 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001329984.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRGAP2C	NM_001329984.2	MANE Select	c.487-3780C>T		intron	N/A	NP_001316913.1
	SRGAP2C	NM_001271872.3		c.487-3780C>T		intron	N/A	NP_001258801.1
	SRGAP2-AS1	NR_104189.1		n.330-7303G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRGAP2C	ENST00000367123.8	TSL:5 MANE Select	c.487-3780C>T		intron	N/A	ENSP00000478290.1
	SRGAP2C	ENST00000304465.7	TSL:5	c.28-3780C>T		intron	N/A	ENSP00000483477.1
	SRGAP2-AS1	ENST00000437515.1	TSL:2	n.330-7303G>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 7

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 7

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.5
DANN	Benign	0.91
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs2580520; hg19: chr1-121112052;