rs911213

chr1-33829106-G-Achr1-33829106-G-Cchr1-33829106-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001281956.2(CSMD2):c.1034-3332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,136 control chromosomes in the GnomAD database, including 47,771 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 0.79 (47771 hom., cov: 32)
• Consequence: CSMD2 NM_001281956.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSMD2	NM_001281956.2	c.1034-3332C>T		intron_variant		ENST00000373381.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSMD2	ENST00000373381.9	c.1034-3332C>T		intron_variant		1	NM_001281956.2	P2
CSMD2	ENST00000373388.7	c.914-3332C>T		intron_variant		1
CSMD2	ENST00000619121.4	c.914-3332C>T		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119382 AN: 152018 Hom.: 47719 Cov.: 32

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.785 AC: 119494 AN: 152136 Hom.: 47771 Cov.: 32 AF XY: 0.790 AC XY: 58775 AN XY: 74354

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.776

Alfa AF: 0.721 Hom.: 25557

Bravo AF: 0.799

Asia WGS AF: 0.920 AC: 3201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.73
Dann	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs911213; hg19: chr1-34294707;