NM_001281956.2:c.517+32740A>G

Variant names:

• chr1-33999854-T-C
• rs9425977
• NM_001281956.2:c.517+32740A>G

Variant summary

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

The NM_001281956.2(CSMD2):​c.517+32740A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,314 control chromosomes in the GnomAD database, including 422 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 0.067 (422 hom., cov: 32)
• Consequence: CSMD2 NM_001281956.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 1 publications found

Genes affected

CSMD2 (HGNC:19290): (CUB and Sushi multiple domains 2) The protein encoded by this gene is thought to be involved in the control of complement cascade of the immune system. Defects in this gene have been associated with schizophrenia. This gene may act as a tumor suppressor for colorectal cancer. [provided by RefSeq, Jan 2020]

ENSG00000295180 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001281956.2. 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
	CSMD2	NM_001281956.2	MANE Select	c.517+32740A>G		intron	N/A	NP_001268885.1
	CSMD2	NM_052896.5		c.397+32740A>G		intron	N/A	NP_443128.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSMD2	ENST00000373381.9	TSL:1 MANE Select	c.517+32740A>G		intron	N/A	ENSP00000362479.4
	CSMD2	ENST00000373388.7	TSL:1	c.397+32740A>G		intron	N/A	ENSP00000362486.3
	CSMD2	ENST00000619121.4	TSL:5	c.397+32740A>G		intron	N/A	ENSP00000483463.1

Frequencies

GnomAD3 genomes AF: 0.0669 AC: 10176 AN: 152196 Hom.: 421 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0668 AC: 10179 AN: 152314 Hom.: 422 Cov.: 32 AF XY: 0.0637 AC XY: 4746 AN XY: 74488

African (AFR) AF: 0.105 AC: 4365 AN: 41546

American (AMR) AF: 0.0497 AC: 760 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0854 AC: 296 AN: 3468

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5188

South Asian (SAS) AF: 0.0362 AC: 175 AN: 4832

European-Finnish (FIN) AF: 0.0412 AC: 438 AN: 10626

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0564 AC: 3840 AN: 68028

Other (OTH) AF: 0.0738 AC: 156 AN: 2114

Alfa AF: 0.0659 Hom.: 581

Bravo AF: 0.0714

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.84
PhyloP100		0.13
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: rs9425977; hg19: chr1-34465455;