rs57521028

Variant names:

• chr19-7610597-C-T
• rs57521028
• NM_020902.2:c.882C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-7610597-C-T
• chr19-7610597-C-A

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_020902.2(CAMSAP3):​c.882C>T​(p.Tyr294Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00606 in 1,613,128 control chromosomes in the GnomAD database, including 500 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.033 (272 hom., cov: 32)
  • Exomes 𝑓: 0.0033 (228 hom.)
• Consequence: CAMSAP3 NM_020902.2 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0280
• Publications: 1 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 -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BP6: Variant 19-7610597-C-T is Benign according to our data. Variant chr19-7610597-C-T is described in ClinVar as Benign. ClinVar VariationId is 768958.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.028 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020902.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMSAP3	NM_020902.2	MANE Select	c.882C>T	p.Tyr294Tyr	synonymous	Exon 6 of 17	NP_065953.1	Q9P1Y5-1
	CAMSAP3	NM_001080429.3		c.963C>T	p.Tyr321Tyr	synonymous	Exon 8 of 19	NP_001073898.1	Q9P1Y5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMSAP3	ENST00000160298.9	TSL:2 MANE Select	c.882C>T	p.Tyr294Tyr	synonymous	Exon 6 of 17	ENSP00000160298.3	Q9P1Y5-1
	CAMSAP3	ENST00000446248.4	TSL:1	c.963C>T	p.Tyr321Tyr	synonymous	Exon 8 of 19	ENSP00000416797.1	Q9P1Y5-2
	CAMSAP3	ENST00000930508.1		c.882C>T	p.Tyr294Tyr	synonymous	Exon 6 of 17	ENSP00000600567.1

Frequencies

GnomAD3 genomes AF: 0.0326 AC: 4962 AN: 152158 Hom.: 272 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0125

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000413

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000294

Gnomad OTH AF: 0.0191

GnomAD2 exomes AF: 0.00804 AC: 1995 AN: 248044 AF XY: 0.00617

Gnomad AFR exome AF: 0.113

Gnomad AMR exome AF: 0.00571

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000187

Gnomad OTH exome AF: 0.00364

GnomAD4 exome AF: 0.00330 AC: 4814 AN: 1460852 Hom.: 228 Cov.: 35 AF XY: 0.00282 AC XY: 2048 AN XY: 726748

African (AFR) AF: 0.117 AC: 3933 AN: 33480

American (AMR) AF: 0.00635 AC: 284 AN: 44708

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26110

East Asian (EAS) AF: 0.0000504 AC: 2 AN: 39700

South Asian (SAS) AF: 0.000243 AC: 21 AN: 86250

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52752

Middle Eastern (MID) AF: 0.00468 AC: 27 AN: 5766

European-Non Finnish (NFE) AF: 0.000162 AC: 180 AN: 1111724

Other (OTH) AF: 0.00608 AC: 367 AN: 60362

GnomAD4 genome AF: 0.0326 AC: 4963 AN: 152276 Hom.: 272 Cov.: 32 AF XY: 0.0312 AC XY: 2327 AN XY: 74466

African (AFR) AF: 0.113 AC: 4709 AN: 41534

American (AMR) AF: 0.0125 AC: 191 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000414 AC: 2 AN: 4834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000294 AC: 20 AN: 68016

Other (OTH) AF: 0.0189 AC: 40 AN: 2114

Alfa AF: 0.0145 Hom.: 53

Bravo AF: 0.0370

Asia WGS AF: 0.00780 AC: 27 AN: 3476

EpiCase AF: 0.000327

EpiControl AF: 0.000356

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	0.83
DANN	Benign	0.22
PhyloP100		-0.028
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs57521028; hg19: chr19-7675483;