8-4352618-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033225.6(CSMD1):c.415+67335G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,070 control chromosomes in the GnomAD database, including 28,181 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 0.59 (28181 hom., cov: 33)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSMD1	NM_033225.6	c.415+67335G>C		intron_variant		ENST00000635120.2
CSMD1	XM_011534752.3	c.415+67335G>C		intron_variant
CSMD1	XM_017013731.2	c.415+67335G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSMD1	ENST00000635120.2	c.415+67335G>C		intron_variant		5	NM_033225.6	P4

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89716 AN: 151952 Hom.: 28166 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.590 AC: 89765 AN: 152070 Hom.: 28181 Cov.: 33 AF XY: 0.589 AC XY: 43777 AN XY: 74324

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.606

Alfa AF: 0.524 Hom.: 1605

Bravo AF: 0.593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs1560428; hg19: chr8-4210140;