NM_033225.6:c.86-31269A>G

Variant names:

• chr8-4668827-T-C
• rs1038058
• NM_033225.6:c.86-31269A>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.86-31269A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,906 control chromosomes in the GnomAD database, including 22,639 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 0.54 (22639 hom., cov: 31)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSMD1	NM_033225.6	c.86-31269A>G		intron_variant	Intron 1 of 69	ENST00000635120.2	NP_150094.5
CSMD1	XM_011534752.3	c.86-31269A>G		intron_variant	Intron 1 of 68		XP_011533054.1
CSMD1	XM_017013731.2	c.86-31269A>G		intron_variant	Intron 1 of 63		XP_016869220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSMD1	ENST00000635120.2	c.86-31269A>G		intron_variant	Intron 1 of 69	5	NM_033225.6	ENSP00000489225.1

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82470 AN: 151790 Hom.: 22615 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.543 AC: 82540 AN: 151906 Hom.: 22639 Cov.: 31 AF XY: 0.544 AC XY: 40358 AN XY: 74226

African (AFR) AF: 0.530 AC: 21978 AN: 41436

American (AMR) AF: 0.638 AC: 9744 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2105 AN: 3466

East Asian (EAS) AF: 0.559 AC: 2871 AN: 5140

South Asian (SAS) AF: 0.616 AC: 2960 AN: 4808

European-Finnish (FIN) AF: 0.483 AC: 5088 AN: 10536

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35836 AN: 67932

Other (OTH) AF: 0.564 AC: 1188 AN: 2106

Alfa AF: 0.534 Hom.: 13742

Bravo AF: 0.554

Asia WGS AF: 0.602 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		-0.096
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: rs1038058; hg19: chr8-4526349;