rs61743295

Variant names:

• chr13-113190934-C-A
• rs61743295
• NM_001127202.4:c.405G>T

Your query was ambiguous. Multiple possible variants found:

• chr13-113190934-C-A
• chr13-113190934-C-G
• chr13-113190934-C-T

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BS1 BS2

The NM_001127202.4(PCID2):​c.405G>T​(p.Gly135Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,613,538 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0072 (18 hom., cov: 32)
  • Exomes 𝑓: 0.00076 (12 hom.)
• Consequence: PCID2 NM_001127202.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.14
• Publications: 1 publications found

Genes affected

PCID2 (HGNC:25653): (PCI domain containing 2) This gene encodes a component of the TREX-2 complex (transcription and export complex 2), which regulates mRNA export from the nucleus. This protein regulates expression of Mad2 mitotic arrest deficient-like 1, a cell division checkpoint protein. This protein also interacts with and stabilizes Brca2 (breast cancer 2) protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

ACMG classification

Our verdict: Benign. The variant received -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BP6: Variant 13-113190934-C-A is Benign according to our data. Variant chr13-113190934-C-A is described in ClinVar as Benign. ClinVar VariationId is 734849.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-1.14 with no splicing effect.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00719 (1095/152262) while in subpopulation AFR AF = 0.0246 (1024/41548). AF 95% confidence interval is 0.0234. There are 18 homozygotes in GnomAd4. There are 511 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 18 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001127202.4. 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
	PCID2	NM_001127202.4	MANE Select	c.405G>T	p.Gly135Gly	synonymous	Exon 7 of 14	NP_001120674.1	Q5JVF3-1
	PCID2	NM_001320656.2		c.567G>T	p.Gly189Gly	synonymous	Exon 7 of 15	NP_001307585.1	Q5JVF3-4
	PCID2	NM_001320657.2		c.405G>T	p.Gly135Gly	synonymous	Exon 7 of 14	NP_001307586.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCID2	ENST00000337344.9	TSL:2 MANE Select	c.405G>T	p.Gly135Gly	synonymous	Exon 7 of 14	ENSP00000337405.4	Q5JVF3-1
	PCID2	ENST00000375477.5	TSL:1	c.405G>T	p.Gly135Gly	synonymous	Exon 7 of 15	ENSP00000364626.1	Q5JVF3-1
	PCID2	ENST00000375479.6	TSL:2	c.405G>T	p.Gly135Gly	synonymous	Exon 7 of 15	ENSP00000364628.2	Q5JVF3-1

Frequencies

GnomAD3 genomes AF: 0.00718 AC: 1093 AN: 152144 Hom.: 18 Cov.: 32

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00367

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.00478

GnomAD2 exomes AF: 0.00195 AC: 488 AN: 250892 AF XY: 0.00139

Gnomad AFR exome AF: 0.0254

Gnomad AMR exome AF: 0.00163

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000123

Gnomad OTH exome AF: 0.00114

GnomAD4 exome AF: 0.000756 AC: 1105 AN: 1461276 Hom.: 12 Cov.: 30 AF XY: 0.000622 AC XY: 452 AN XY: 726968

African (AFR) AF: 0.0239 AC: 799 AN: 33402

American (AMR) AF: 0.00175 AC: 78 AN: 44660

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26124

East Asian (EAS) AF: 0.00 AC: 0 AN: 39660

South Asian (SAS) AF: 0.0000348 AC: 3 AN: 86180

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53412

Middle Eastern (MID) AF: 0.00156 AC: 9 AN: 5768

European-Non Finnish (NFE) AF: 0.000110 AC: 122 AN: 1111686

Other (OTH) AF: 0.00156 AC: 94 AN: 60384

GnomAD4 genome AF: 0.00719 AC: 1095 AN: 152262 Hom.: 18 Cov.: 32 AF XY: 0.00686 AC XY: 511 AN XY: 74456

African (AFR) AF: 0.0246 AC: 1024 AN: 41548

American (AMR) AF: 0.00366 AC: 56 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00 AC: 0 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

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

European-Non Finnish (NFE) AF: 0.0000588 AC: 4 AN: 68004

Other (OTH) AF: 0.00473 AC: 10 AN: 2116

Alfa AF: 0.00274 Hom.: 1

Bravo AF: 0.00819

Asia WGS AF: 0.00144 AC: 5 AN: 3478

EpiCase AF: 0.000164

EpiControl AF: 0.000297

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	-0.29
CADD	Benign	6.6
DANN	Benign	0.63
PhyloP100		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=93/7	polymorphism

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: rs61743295; hg19: chr13-113845248;