rs34100269

Variant names:

• chr4-761398-C-T
• rs34100269
• NM_006315.7:c.582C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-761398-C-T
• chr4-761398-C-A
• chr4-761398-C-G

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_006315.7(PCGF3):​c.582C>T​(p.Asn194Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00312 in 1,608,522 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0045 (4 hom., cov: 33)
  • Exomes 𝑓: 0.0030 (13 hom.)
• Consequence: PCGF3 NM_006315.7 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.918
• Publications: 1 publications found

Genes affected

PCGF3 (HGNC:10066): (polycomb group ring finger 3) The protein encoded by this gene contains a C3HC4 type RING finger, which is a motif known to be involved in protein-protein interactions. The specific function of this protein has not yet been determined. [provided by RefSeq, Jul 2008]

LOC124900163 (HGNC:):

PCGF3-AS1 (HGNC:56108): (PCGF3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP6: Variant 4-761398-C-T is Benign according to our data. Variant chr4-761398-C-T is described in ClinVar as Benign. ClinVar VariationId is 769626.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.918 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 4 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006315.7. 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
	PCGF3	NM_006315.7	MANE Select	c.582C>T	p.Asn194Asn	synonymous	Exon 9 of 11	NP_006306.2
	PCGF3	NM_001317836.3		c.582C>T	p.Asn194Asn	synonymous	Exon 10 of 12	NP_001304765.1	Q3KNV8-1
	PCGF3	NM_001395245.1		c.582C>T	p.Asn194Asn	synonymous	Exon 10 of 12	NP_001382174.1	Q3KNV8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCGF3	ENST00000362003.10	TSL:5 MANE Select	c.582C>T	p.Asn194Asn	synonymous	Exon 9 of 11	ENSP00000354724.5	Q3KNV8-1
	PCGF3	ENST00000470161.6	TSL:1	c.582C>T	p.Asn194Asn	synonymous	Exon 9 of 11	ENSP00000420489.2	Q3KNV8-1
	PCGF3	ENST00000870362.1		c.582C>T	p.Asn194Asn	synonymous	Exon 10 of 12	ENSP00000540421.1

Frequencies

GnomAD3 genomes AF: 0.00447 AC: 680 AN: 152256 Hom.: 4 Cov.: 33

Gnomad AFR AF: 0.00543

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0124

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00451

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.00313 AC: 766 AN: 244652 AF XY: 0.00304

Gnomad AFR exome AF: 0.00673

Gnomad AMR exome AF: 0.000635

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000571

Gnomad FIN exome AF: 0.0111

Gnomad NFE exome AF: 0.00335

Gnomad OTH exome AF: 0.00153

GnomAD4 exome AF: 0.00298 AC: 4342 AN: 1456148 Hom.: 13 Cov.: 31 AF XY: 0.00301 AC XY: 2182 AN XY: 724026

African (AFR) AF: 0.00628 AC: 209 AN: 33278

American (AMR) AF: 0.000637 AC: 28 AN: 43978

Ashkenazi Jewish (ASJ) AF: 0.000308 AC: 8 AN: 26014

East Asian (EAS) AF: 0.0000510 AC: 2 AN: 39244

South Asian (SAS) AF: 0.000574 AC: 49 AN: 85322

European-Finnish (FIN) AF: 0.0109 AC: 579 AN: 53298

Middle Eastern (MID) AF: 0.000174 AC: 1 AN: 5748

European-Non Finnish (NFE) AF: 0.00301 AC: 3335 AN: 1109088

Other (OTH) AF: 0.00218 AC: 131 AN: 60178

GnomAD4 genome AF: 0.00448 AC: 682 AN: 152374 Hom.: 4 Cov.: 33 AF XY: 0.00484 AC XY: 361 AN XY: 74510

African (AFR) AF: 0.00543 AC: 226 AN: 41594

American (AMR) AF: 0.000588 AC: 9 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4830

European-Finnish (FIN) AF: 0.0124 AC: 132 AN: 10624

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

European-Non Finnish (NFE) AF: 0.00451 AC: 307 AN: 68042

Other (OTH) AF: 0.00284 AC: 6 AN: 2114

Alfa AF: 0.00343 Hom.: 1

Bravo AF: 0.00338

Asia WGS AF: 0.00115 AC: 4 AN: 3478

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	-0.62
CADD	Benign	14
DANN	Benign	0.66
PhyloP100		0.92
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)		0.0		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: rs34100269; hg19: chr4-755186;