NM_033225.6:c.1010-39018A>G

Variant names:

• chr8-3655815-T-C
• rs2469390
• NM_033225.6:c.1010-39018A>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.1010-39018A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,046 control chromosomes in the GnomAD database, including 46,053 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 0.78 (46053 hom., cov: 31)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSMD1	NM_033225.6	c.1010-39018A>G		intron_variant	Intron 7 of 69	ENST00000635120.2	NP_150094.5
CSMD1	XM_011534752.3	c.1010-39018A>G		intron_variant	Intron 7 of 68		XP_011533054.1
CSMD1	XM_017013731.2	c.1010-39018A>G		intron_variant	Intron 7 of 63		XP_016869220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSMD1	ENST00000635120.2	c.1010-39018A>G		intron_variant	Intron 7 of 69	5	NM_033225.6	ENSP00000489225.1

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117877 AN: 151928 Hom.: 46040 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.776 AC: 117945 AN: 152046 Hom.: 46053 Cov.: 31 AF XY: 0.775 AC XY: 57639 AN XY: 74328

African (AFR) AF: 0.693 AC: 28695 AN: 41426

American (AMR) AF: 0.765 AC: 11691 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2733 AN: 3472

East Asian (EAS) AF: 0.695 AC: 3577 AN: 5150

South Asian (SAS) AF: 0.733 AC: 3535 AN: 4822

European-Finnish (FIN) AF: 0.843 AC: 8923 AN: 10580

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56087 AN: 67994

Other (OTH) AF: 0.784 AC: 1653 AN: 2108

Alfa AF: 0.807 Hom.: 80499

Bravo AF: 0.765

Asia WGS AF: 0.724 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.55
DANN	Benign	0.63
PhyloP100		-0.79
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: rs2469390; hg19: chr8-3513337;