NM_001385503.1:c.2289G>A

Variant names:

• chr12-30715074-C-T
• rs78303008
• NM_001385503.1:c.2289G>A

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_Moderate BP6_Very_Strong BP7 BS2

The NM_001385503.1(CAPRIN2):​c.2289G>A​(p.Thr763Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00842 in 1,613,880 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0059 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0087 (50 hom.)
• Consequence: CAPRIN2 NM_001385503.1 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0560
• Publications: 4 publications found

Genes affected

CAPRIN2 (HGNC:21259): (caprin family member 2) The protein encoded by this gene may regulate the transport of mRNA. It may play a role in the differentiation of erythroblasts. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

ACMG classification

Our verdict: Benign. The variant received -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BP6: Variant 12-30715074-C-T is Benign according to our data. Variant chr12-30715074-C-T is described in ClinVar as Benign. ClinVar VariationId is 779266.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.056 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385503.1. 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
	CAPRIN2	NM_001385503.1	MANE Select	c.2289G>A	p.Thr763Thr	synonymous	Exon 16 of 19	NP_001372432.1	F5H5J8
	CAPRIN2	NM_001002259.3		c.2535G>A	p.Thr845Thr	synonymous	Exon 15 of 18	NP_001002259.1	Q6IMN6-1
	CAPRIN2	NM_001319843.2		c.2532G>A	p.Thr844Thr	synonymous	Exon 15 of 18	NP_001306772.1	Q6IMN6-9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPRIN2	ENST00000695402.1	MANE Select	c.2289G>A	p.Thr763Thr	synonymous	Exon 16 of 19	ENSP00000511883.1	F5H5J8
	CAPRIN2	ENST00000298892.9	TSL:1	c.2385G>A	p.Thr795Thr	synonymous	Exon 14 of 17	ENSP00000298892.5	Q6IMN6-2
	CAPRIN2	ENST00000417045.5	TSL:1	c.2532G>A	p.Thr844Thr	synonymous	Exon 15 of 18	ENSP00000391479.1	Q6IMN6-3

Frequencies

GnomAD3 genomes AF: 0.00588 AC: 895 AN: 152166 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00181

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00393

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.00575

GnomAD2 exomes AF: 0.00558 AC: 1403 AN: 251314 AF XY: 0.00571

Gnomad AFR exome AF: 0.00160

Gnomad AMR exome AF: 0.00286

Gnomad ASJ exome AF: 0.00377

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00351

Gnomad NFE exome AF: 0.00978

Gnomad OTH exome AF: 0.00473

GnomAD4 exome AF: 0.00869 AC: 12700 AN: 1461596 Hom.: 50 Cov.: 32 AF XY: 0.00848 AC XY: 6168 AN XY: 727116

African (AFR) AF: 0.00149 AC: 50 AN: 33464

American (AMR) AF: 0.00315 AC: 141 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.00360 AC: 94 AN: 26126

East Asian (EAS) AF: 0.00 AC: 0 AN: 39686

South Asian (SAS) AF: 0.00108 AC: 93 AN: 86252

European-Finnish (FIN) AF: 0.00346 AC: 185 AN: 53418

Middle Eastern (MID) AF: 0.00399 AC: 23 AN: 5768

European-Non Finnish (NFE) AF: 0.0105 AC: 11724 AN: 1111780

Other (OTH) AF: 0.00646 AC: 390 AN: 60382

GnomAD4 genome AF: 0.00588 AC: 895 AN: 152284 Hom.: 3 Cov.: 32 AF XY: 0.00517 AC XY: 385 AN XY: 74466

African (AFR) AF: 0.00180 AC: 75 AN: 41562

American (AMR) AF: 0.00392 AC: 60 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4830

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10608

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0104 AC: 709 AN: 68028

Other (OTH) AF: 0.00569 AC: 12 AN: 2110

Alfa AF: 0.00642 Hom.: 3

Bravo AF: 0.00572

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.0103

EpiControl AF: 0.0105

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	-0.30
CADD	Benign	12
DANN	Benign	0.65
PhyloP100		-0.056
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs78303008; hg19: chr12-30868008; COSMIC: COSV108026125; COSMIC: COSV108026125;