Variant rs10505168 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000297405.10(CSMD3):c.3310+1586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 169,910 control chromosomes in the GnomAD database, including 11,265 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 0.35 ( 10179 hom., cov: 32)

Exomes 𝑓: 0.35 ( 1086 hom. )

Consequence

CSMD3
ENST00000297405.10 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.470

Variant links:

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 links:

MIR2053 (HGNC:37069): (microRNA 2053) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR2053 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSMD3	NM_198123.2 linkuse as main transcript	c.3310+1586A>G		intron_variant		ENST00000297405.10	NP_937756.1
MIR2053	NR_031745.1 linkuse as main transcript	n.31T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSMD3	ENST00000297405.10 linkuse as main transcript	c.3310+1586A>G		intron_variant		1	NM_198123.2	ENSP00000297405	P1	Q7Z407-1
MIR2053	ENST00000459295.1 linkuse as main transcript	n.31T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.353

AC:

53610

AN:

151818

Hom.:

10169

Cov.:

show subpopulations

Gnomad AFR

AF:

0.500

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.419

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.316

GnomAD3 exomes

AF:

0.330

AC:

7757

AN:

23476

Hom.:

1334

AF XY:

0.322

AC XY:

3374

AN XY:

10476

show subpopulations

Gnomad AFR exome

AF:

0.480

Gnomad AMR exome

AF:

0.286

Gnomad ASJ exome

AF:

0.254

Gnomad EAS exome

AF:

0.448

Gnomad SAS exome

AF:

0.269

Gnomad FIN exome

AF:

0.354

Gnomad NFE exome

AF:

0.283

Gnomad OTH exome

AF:

0.261

GnomAD4 exome

AF:

0.348

AC:

6251

AN:

17974

Hom.:

1086

Cov.:

AF XY:

0.343

AC XY:

2954

AN XY:

8604

show subpopulations

Gnomad4 AFR exome

AF:

0.446

Gnomad4 AMR exome

AF:

0.167

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.289

Gnomad4 FIN exome

AF:

0.358

Gnomad4 NFE exome

AF:

0.308

Gnomad4 OTH exome

AF:

0.353

GnomAD4 genome

AF:

0.353

AC:

53662

AN:

151936

Hom.:

10179

Cov.:

AF XY:

0.357

AC XY:

26507

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.499

Gnomad4 AMR

AF:

0.316

Gnomad4 ASJ

AF:

0.269

Gnomad4 EAS

AF:

0.420

Gnomad4 SAS

AF:

0.305

Gnomad4 FIN

AF:

0.344

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.315

Alfa

AF:

0.325

Hom.:

985

Bravo

AF:

0.360

Asia WGS

AF:

0.369

AC:

1282

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over