7-143756089-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_178561.5(CTAGE6):​c.1570G>C​(p.Ala524Pro) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A524S) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 9)
  • Exomes 𝑓: 9.6e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CTAGE6 NM_178561.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.09675643).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTAGE6	NM_178561.5	c.1570G>C	p.Ala524Pro	missense_variant	Exon 1 of 1	ENST00000470691.2	NP_848656.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTAGE6	ENST00000470691.2	c.1570G>C	p.Ala524Pro	missense_variant	Exon 1 of 1	6	NM_178561.5	ENSP00000474388.1
ENSG00000291149	ENST00000700950.1	n.178+13009G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 9

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.62e-7 AC: 1 AN: 1039200 Hom.: 0 Cov.: 17 AF XY: 0.00000194 AC XY: 1 AN XY: 515710

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000294

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 9

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	2.6
DANN	Benign	0.32
DEOGEN2	Benign	0.070	T
FATHMM_MKL	Benign	0.019	N
M_CAP	Benign	0.0087	T
MetaRNN	Benign	0.097	T
MutationAssessor	Benign	0.0	N
PrimateAI	Uncertain	0.50	T
Sift4G	Benign	0.20	T
Polyphen		0.58	P
Vest4		0.11
MVP		0.14
GERP RS		-0.22
Varity_R		0.10
gMVP		0.44

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: rs764189306; hg19: chr7-143453182;