rs4875610

Variant names:

• chr8-3320389-C-A
• rs4875610
• NM_033225.6:c.3632-11886G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-3320389-C-A
• chr8-3320389-C-G
• chr8-3320389-C-T

Variant summary

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

The NM_033225.6(CSMD1):​c.3632-11886G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,858 control chromosomes in the GnomAD database, including 13,095 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 0.41 (13095 hom., cov: 32)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 2 publications found

Genes affected

CSMD1 (HGNC:14026): (CUB and Sushi multiple domains 1) Predicted to act upstream of or within several processes, including learning or memory; mammary gland branching involved in pregnancy; and reproductive structure development. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CSMD1 Gene-Disease associations (from GenCC):

• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• complex neurodevelopmental disorder

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033225.6. 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
	CSMD1	NM_033225.6	MANE Select	c.3632-11886G>T		intron	N/A	NP_150094.5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSMD1	ENST00000635120.2	TSL:5 MANE Select	c.3632-11886G>T		intron	N/A	ENSP00000489225.1
	CSMD1	ENST00000335551.11	TSL:1	c.2072-11886G>T		intron	N/A	ENSP00000334828.6
	CSMD1	ENST00000523488.5	TSL:1	n.1165-11886G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62621 AN: 151740 Hom.: 13088 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.413 AC: 62661 AN: 151858 Hom.: 13095 Cov.: 32 AF XY: 0.415 AC XY: 30820 AN XY: 74224

African (AFR) AF: 0.400 AC: 16555 AN: 41392

American (AMR) AF: 0.387 AC: 5905 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3468

East Asian (EAS) AF: 0.468 AC: 2405 AN: 5144

South Asian (SAS) AF: 0.517 AC: 2490 AN: 4816

European-Finnish (FIN) AF: 0.445 AC: 4679 AN: 10524

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27842 AN: 67948

Other (OTH) AF: 0.403 AC: 846 AN: 2098

Alfa AF: 0.405 Hom.: 48086

Bravo AF: 0.407

Asia WGS AF: 0.494 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.71
PhyloP100		0.50
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: rs4875610; hg19: chr8-3177911;