rs11782360

chr8-3098708-A-C

Variant summary

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

The NM_033225.6(CSMD1):c.6950-1671T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,132 control chromosomes in the GnomAD database, including 1,381 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 0.12 (1381 hom., cov: 31)
• Consequence: CSMD1 NM_033225.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSMD1	NM_033225.6	c.6950-1671T>G		intron_variant		ENST00000635120.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSMD1	ENST00000635120.2	c.6950-1671T>G		intron_variant		5	NM_033225.6	P4

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18563 AN: 152014 Hom.: 1384 Cov.: 31

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.122 AC: 18556 AN: 152132 Hom.: 1381 Cov.: 31 AF XY: 0.121 AC XY: 8962 AN XY: 74362

Gnomad4 AFR AF: 0.0546

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0724

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.122

Alfa AF: 0.158 Hom.: 2679

Bravo AF: 0.116

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.14
Dann	Benign	0.69

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: rs11782360; hg19: chr8-2956230;