rs10505170

chr8-112631533-A-T

Variant summary

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

The NM_198123.2(CSMD3):c.3715+5284T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,980 control chromosomes in the GnomAD database, including 1,921 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 0.14 (1921 hom., cov: 33)
• Consequence: CSMD3 NM_198123.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.906

Genes affected

CSMD3 (HGNC:19291): (CUB and Sushi multiple domains 3) Predicted to be involved in regulation of dendrite development. Predicted to be located in plasma 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSMD3	NM_198123.2	c.3715+5284T>A		intron_variant		ENST00000297405.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSMD3	ENST00000297405.10	c.3715+5284T>A		intron_variant		1	NM_198123.2	P1
CSMD3	ENST00000339701.7	c.1735+5284T>A		intron_variant		1
CSMD3	ENST00000343508.7	c.3595+5284T>A		intron_variant		1
CSMD3	ENST00000455883.2	c.3403+5284T>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21026 AN: 151860 Hom.: 1917 Cov.: 33

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.138 AC: 21036 AN: 151980 Hom.: 1921 Cov.: 33 AF XY: 0.144 AC XY: 10672 AN XY: 74282

Gnomad4 AFR AF: 0.0312

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.141

Alfa AF: 0.153 Hom.: 256

Bravo AF: 0.130

Asia WGS AF: 0.0930 AC: 324 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.6
Dann	Benign	0.54

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: rs10505170; hg19: chr8-113643762;