chr6-7329185-G-A

Position:

• chr6-7329185-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP6

The NM_001170693.2(CAGE1):​c.2455C>T​(p.Arg819*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00002 in 399,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.000033 (0 hom., cov: 30)
  • Exomes 𝑓: 0.000012 (0 hom.)
• Consequence: CAGE1 NM_001170693.2 stop_gained
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -2.72

Genes affected

CAGE1 (HGNC:21622): (cancer antigen 1)

SSR1 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 6-7329185-G-A is Benign according to our data. Variant chr6-7329185-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2681693.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAGE1	NM_001170692.2	c.2478+664C>T		intron_variant		ENST00000502583.6	NP_001164163.1
CAGE1	NM_001170693.2	c.2455C>T	p.Arg819*	stop_gained	13/13		NP_001164164.1
CAGE1	NM_205864.3	c.1884+664C>T		intron_variant			NP_995586.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAGE1	ENST00000338150.8	c.2455C>T	p.Arg819*	stop_gained	13/13	2		ENSP00000338107.4
CAGE1	ENST00000502583.6	c.2478+664C>T		intron_variant		5	NM_001170692.2	ENSP00000425493.1
CAGE1	ENST00000379918.8	c.2412+664C>T		intron_variant		5		ENSP00000369250.4
CAGE1	ENST00000512086.5	c.2292+664C>T		intron_variant		5		ENSP00000427583.1
CAGE1	ENST00000296742.11	c.1884+664C>T		intron_variant		1		ENSP00000296742.7
CAGE1	ENST00000442019.6	n.*1744+664C>T		intron_variant		1		ENSP00000391746.2
CAGE1	ENST00000458291.6	n.*430+664C>T		intron_variant		1		ENSP00000390644.2

Frequencies

GnomAD3 genomes AF: 0.0000330 AC: 5 AN: 151738 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000121 AC: 3 AN: 247340 Hom.: 0 Cov.: 0 AF XY: 0.0000236 AC XY: 3 AN XY: 127078

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000895

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000638

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000330 AC: 5 AN: 151738 Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1 AN XY: 74072

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000197

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000642

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma Benign:1

Likely benign, no assertion criteria provided

research

Department of Clinical Pathology, School of Medicine, Fujita Health University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.52	T
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.92
Eigen	Benign	-1.8
Eigen_PC	Benign	-2.0
FATHMM_MKL	Benign	0.00043	N
Vest4		0.0030
GERP RS		-0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs1414911763; hg19: chr6-7329418;