rs17630545

Positions:

• chr8-112253640-T-C

Variant summary

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

The NM_198123.2(CSMD3):​c.10110+613A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,866 control chromosomes in the GnomAD database, including 3,001 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 0.18 (3001 hom., cov: 32)
• Consequence: CSMD3 NM_198123.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

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]

CSMD3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSMD3	NM_198123.2	c.10110+613A>G		intron_variant		ENST00000297405.10	NP_937756.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSMD3	ENST00000297405.10	c.10110+613A>G		intron_variant		1	NM_198123.2	ENSP00000297405.5

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28059 AN: 151748 Hom.: 3002 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0833

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.185 AC: 28060 AN: 151866 Hom.: 3001 Cov.: 32 AF XY: 0.183 AC XY: 13592 AN XY: 74202

Gnomad4 AFR AF: 0.0907

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.0837

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.211

Alfa AF: 0.228 Hom.: 7014

Bravo AF: 0.175

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	8.2
DANN	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs17630545; hg19: chr8-113265869;