rs10094349

Variant names:

• chr8-4332790-T-C
• rs10094349
• NM_033225.6:c.415+87163A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-4332790-T-C
• chr8-4332790-T-G

Variant summary

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

The NM_033225.6(CSMD1):​c.415+87163A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,840 control chromosomes in the GnomAD database, including 16,755 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 0.45 (16755 hom., cov: 31)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSMD1	NM_033225.6	MANE Select	c.415+87163A>G		intron	N/A	NP_150094.5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSMD1	ENST00000635120.2	TSL:5 MANE Select	c.415+87163A>G		intron	N/A	ENSP00000489225.1	Q96PZ7-1
	CSMD1	ENST00000520002.5	TSL:5	c.415+87163A>G		intron	N/A	ENSP00000430733.1	E5RIG2
	CSMD1	ENST00000602557.5	TSL:5	c.415+87163A>G		intron	N/A	ENSP00000473359.1	E5RIG2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67805 AN: 151722 Hom.: 16732 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.447 AC: 67867 AN: 151840 Hom.: 16755 Cov.: 31 AF XY: 0.450 AC XY: 33402 AN XY: 74184

African (AFR) AF: 0.666 AC: 27577 AN: 41404

American (AMR) AF: 0.289 AC: 4408 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1322 AN: 3464

East Asian (EAS) AF: 0.318 AC: 1634 AN: 5136

South Asian (SAS) AF: 0.468 AC: 2253 AN: 4812

European-Finnish (FIN) AF: 0.498 AC: 5243 AN: 10528

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24086 AN: 67928

Other (OTH) AF: 0.433 AC: 914 AN: 2112

Alfa AF: 0.325 Hom.: 2091

Bravo AF: 0.435

Asia WGS AF: 0.438 AC: 1528 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.64
PhyloP100		0.38
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10094349;

hg19: chr8-4190312;