rs16835611

Variant names:

• chr1-33576185-G-A
• rs16835611
• NM_001281956.2:c.7576+1111C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-33576185-G-A
• chr1-33576185-G-T

Variant summary

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

The NM_001281956.2(CSMD2):​c.7576+1111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,174 control chromosomes in the GnomAD database, including 1,416 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 0.12 (1416 hom., cov: 32)
• Consequence: CSMD2 NM_001281956.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSMD2	NM_001281956.2	c.7576+1111C>T		intron_variant	Intron 49 of 70	ENST00000373381.9	NP_001268885.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSMD2	ENST00000373381.9	c.7576+1111C>T		intron_variant	Intron 49 of 70	1	NM_001281956.2	ENSP00000362479.4
CSMD2	ENST00000373388.7	c.7582+1111C>T		intron_variant	Intron 50 of 69	1		ENSP00000362486.3
CSMD2	ENST00000619121.4	c.7456+1111C>T		intron_variant	Intron 49 of 70	5		ENSP00000483463.1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18574 AN: 152056 Hom.: 1417 Cov.: 32

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.122 AC: 18569 AN: 152174 Hom.: 1416 Cov.: 32 AF XY: 0.119 AC XY: 8835 AN XY: 74378

African (AFR) AF: 0.0333 AC: 1382 AN: 41514

American (AMR) AF: 0.106 AC: 1613 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3472

East Asian (EAS) AF: 0.235 AC: 1215 AN: 5180

South Asian (SAS) AF: 0.121 AC: 584 AN: 4820

European-Finnish (FIN) AF: 0.126 AC: 1333 AN: 10592

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11640 AN: 68000

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.130 Hom.: 250

Bravo AF: 0.117

Asia WGS AF: 0.167 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.70
PhyloP100		1.1
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: rs16835611; hg19: chr1-34041785;