Genetic Variant NM_020902.2:c.3113-58G>T (chr19-7616465-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_020902.2(CAMSAP3):c.3113-58G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CAMSAP3
NM_020902.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.712

Publications

15 publications found

Variant links:

Genes affected

CAMSAP3 (HGNC:29307): (calmodulin regulated spectrin associated protein family member 3) Enables actin filament binding activity and microtubule minus-end binding activity. Involved in several processes, including microtubule cytoskeleton organization; regulation of organelle organization; and zonula adherens maintenance. Located in cytoplasm; nucleoplasm; and zonula adherens. Colocalizes with centrosome and microtubule minus-end. [provided by Alliance of Genome Resources, Apr 2022]

CAMSAP3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMSAP3	NM_020902.2 link	c.3113-58G>T		intron_variant	Intron 13 of 16	ENST00000160298.9	NP_065953.1	Q9P1Y5-1
CAMSAP3	NM_001080429.3 link	c.3194-58G>T		intron_variant	Intron 15 of 18		NP_001073898.1	Q9P1Y5-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CAMSAP3	ENST00000160298.9 link	c.3113-58G>T	intron_variant	Intron 13 of 16	2	NM_020902.2	ENSP00000160298.3	Q9P1Y5-1
CAMSAP3	ENST00000446248.4 link	c.3194-58G>T	intron_variant	Intron 15 of 18	1		ENSP00000416797.1	Q9P1Y5-2
CAMSAP3	ENST00000593434.1 link	n.60G>T	non_coding_transcript_exon_variant	Exon 1 of 2	3
CAMSAP3	ENST00000595692.1 link	n.992-58G>T	intron_variant	Intron 2 of 5	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1040092

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

535678

African (AFR)

AF:

0.00

AC:

AN:

25078

American (AMR)

AF:

0.00

AC:

AN:

43964

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23288

East Asian (EAS)

AF:

0.00

AC:

AN:

37356

South Asian (SAS)

AF:

0.00

AC:

AN:

77666

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51858

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4896

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

729604

Other (OTH)

AF:

0.00

AC:

AN:

46382

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

4127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.66

(source)

DANN

Benign

0.74

PhyloP100

-0.71

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over