NM_020902.2:c.3113-58G>C

Variant names:

• chr19-7616465-G-C
• rs807812
• NM_020902.2:c.3113-58G>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_020902.2(CAMSAP3):​c.3113-58G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000577 in 1,040,092 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000058 (0 hom.)
• Consequence: CAMSAP3 NM_020902.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 15 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000577 AC: 6 AN: 1040092 Hom.: 0 Cov.: 14 AF XY: 0.00000560 AC XY: 3 AN XY: 535678

African (AFR) AF: 0.00 AC: 0 AN: 25078

American (AMR) AF: 0.00 AC: 0 AN: 43964

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23288

East Asian (EAS) AF: 0.00 AC: 0 AN: 37356

South Asian (SAS) AF: 0.00 AC: 0 AN: 77666

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51858

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4896

European-Non Finnish (NFE) AF: 0.00000822 AC: 6 AN: 729604

Other (OTH) AF: 0.00 AC: 0 AN: 46382

GnomAD4 genome Cov.: 32

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	-0.90
CADD	Benign	0.67
DANN	Benign	0.70
PhyloP100		-0.71
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.17		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs807812; hg19: chr19-7681351;