rs764189306

Variant names:

• chr7-143756089-C-A
• rs764189306
• NM_178561.5:c.1570G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-143756089-C-A
• chr7-143756089-C-G
• chr7-143756089-C-T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_178561.5(CTAGE6):​c.1570G>T​(p.Ala524Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00039 (0 hom., cov: 9)
  • Exomes 𝑓: 0.00096 (45 hom.)
  • Failed GnomAD Quality Control
• Consequence: CTAGE6 NM_178561.5 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.965
• Publications: 1 publications found

Genes affected

CTAGE6 (HGNC:28644): (CTAGE family member 6) Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; protein secretion; and vesicle cargo loading. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum exit site and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000291149 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.00538826).
• BP6: Variant 7-143756089-C-A is Benign according to our data. Variant chr7-143756089-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2658120.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178561.5. 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
	CTAGE6	NM_178561.5	MANE Select	c.1570G>T	p.Ala524Ser	missense	Exon 1 of 1	NP_848656.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTAGE6	ENST00000470691.2	TSL:6 MANE Select	c.1570G>T	p.Ala524Ser	missense	Exon 1 of 1	ENSP00000474388.1	Q86UF2
	ENSG00000291149	ENST00000700950.2		n.180+13009G>T		intron	N/A
	ENSG00000291149	ENST00000838407.1		n.212+5695G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000388 AC: 30 AN: 77308 Hom.: 0 Cov.: 9

Gnomad AFR AF: 0.0000929

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000316

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00369

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000544

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000817 AC: 54 AN: 66094 AF XY: 0.000982

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000643

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000125

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000709

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000964 AC: 1000 AN: 1037796 Hom.: 45 Cov.: 17 AF XY: 0.00120 AC XY: 617 AN XY: 514880

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000835 AC: 2 AN: 23940

American (AMR) AF: 0.000814 AC: 17 AN: 20872

Ashkenazi Jewish (ASJ) AF: 0.000115 AC: 2 AN: 17358

East Asian (EAS) AF: 0.000706 AC: 24 AN: 33998

South Asian (SAS) AF: 0.00546 AC: 301 AN: 55140

European-Finnish (FIN) AF: 0.0000791 AC: 3 AN: 37916

Middle Eastern (MID) AF: 0.00265 AC: 8 AN: 3024

European-Non Finnish (NFE) AF: 0.000751 AC: 601 AN: 800682

Other (OTH) AF: 0.000936 AC: 42 AN: 44866

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000388 AC: 30 AN: 77380 Hom.: 0 Cov.: 9 AF XY: 0.000285 AC XY: 10 AN XY: 35100

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000925 AC: 2 AN: 21614

American (AMR) AF: 0.000315 AC: 2 AN: 6346

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1828

East Asian (EAS) AF: 0.00 AC: 0 AN: 2966

South Asian (SAS) AF: 0.00370 AC: 6 AN: 1622

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4596

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 208

European-Non Finnish (NFE) AF: 0.000544 AC: 20 AN: 36738

Other (OTH) AF: 0.00 AC: 0 AN: 926

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000000000000333067), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.000391 Hom.: 0

ExAC AF: 0.0000475 AC: 3

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.60	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	0.010
DANN	Benign	0.38
DEOGEN2	Benign	0.046	T
FATHMM_MKL	Benign	0.0025	N
M_CAP	Benign	0.041	D
MetaRNN	Benign	0.0054	T
MutationAssessor	Benign	-2.9	N
PhyloP100		0.96
PrimateAI	Uncertain	0.48	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.043
MVP		0.15
GERP RS		-0.22
Varity_R		0.076
gMVP		0.30
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: rs764189306; hg19: chr7-143453182;