rs17343819

Variant names:

• chr8-67484680-T-C
• rs17343819
• NM_020361.5:c.746A>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_020361.5(CPA6):​c.746A>G​(p.Asn249Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,514,380 control chromosomes in the GnomAD database, including 14,764 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/25 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N249I) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.11 (1133 hom., cov: 32)
  • Exomes 𝑓: 0.14 (13631 hom.)
• Consequence: CPA6 NM_020361.5 missense, splice_region
• Scores: Splicing: ADA: 0.1073
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:6
• Conservation: PhyloP100: 1.10
• Publications: 20 publications found

Genes affected

CPA6 (HGNC:17245): (carboxypeptidase A6) The gene encodes a member of the peptidase M14 family of metallocarboxypeptidases. The encoded preproprotein is proteolytically processed to generate the mature enzyme, which catalyzes the release of large hydrophobic C-terminal amino acids. This enzyme has functions ranging from digestion of food to selective biosynthesis of neuroendocrine peptides. Mutations in this gene may be linked to epilepsy and febrile seizures, and a translocation t(6;8)(q26;q13) involving this gene has been associated with Duane retraction syndrome. [provided by RefSeq, May 2016]

ARFGEF1-DT (HGNC:55237): (ARFGEF1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0019486845).
• BP6: Variant 8-67484680-T-C is Benign according to our data. Variant chr8-67484680-T-C is described in ClinVar as Benign. ClinVar VariationId is 128847.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020361.5. 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
	CPA6	NM_020361.5	MANE Select	c.746A>G	p.Asn249Ser	missense splice_region	Exon 7 of 11	NP_065094.3
	ARFGEF1-DT	NR_136224.1		n.694-6285T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPA6	ENST00000297770.10	TSL:1 MANE Select	c.746A>G	p.Asn249Ser	missense splice_region	Exon 7 of 11	ENSP00000297770.4	Q8N4T0-1
	CPA6	ENST00000479862.6	TSL:1	n.*342A>G		splice_region non_coding_transcript_exon	Exon 6 of 8	ENSP00000419016.2	Q8N4T0-3
	CPA6	ENST00000518549.1	TSL:1	n.960A>G		splice_region non_coding_transcript_exon	Exon 7 of 8

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17099 AN: 152124 Hom.: 1135 Cov.: 32

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0720

Gnomad FIN AF: 0.0707

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.136

GnomAD2 exomes AF: 0.112 AC: 27734 AN: 247030 AF XY: 0.115

Gnomad AFR exome AF: 0.0598

Gnomad AMR exome AF: 0.0911

Gnomad ASJ exome AF: 0.183

Gnomad EAS exome AF: 0.000773

Gnomad FIN exome AF: 0.0772

Gnomad NFE exome AF: 0.151

Gnomad OTH exome AF: 0.142

GnomAD4 exome AF: 0.135 AC: 184404 AN: 1362138 Hom.: 13631 Cov.: 20 AF XY: 0.135 AC XY: 92233 AN XY: 683486

African (AFR) AF: 0.0584 AC: 1831 AN: 31366

American (AMR) AF: 0.0962 AC: 4203 AN: 43668

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 4444 AN: 25358

East Asian (EAS) AF: 0.000612 AC: 24 AN: 39192

South Asian (SAS) AF: 0.0831 AC: 6934 AN: 83400

European-Finnish (FIN) AF: 0.0780 AC: 4156 AN: 53294

Middle Eastern (MID) AF: 0.232 AC: 1284 AN: 5536

European-Non Finnish (NFE) AF: 0.150 AC: 153808 AN: 1023280

Other (OTH) AF: 0.135 AC: 7720 AN: 57044

GnomAD4 genome AF: 0.112 AC: 17092 AN: 152242 Hom.: 1133 Cov.: 32 AF XY: 0.108 AC XY: 8039 AN XY: 74442

African (AFR) AF: 0.0610 AC: 2533 AN: 41548

American (AMR) AF: 0.122 AC: 1857 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.0727 AC: 351 AN: 4830

European-Finnish (FIN) AF: 0.0707 AC: 750 AN: 10612

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10469 AN: 68008

Other (OTH) AF: 0.135 AC: 284 AN: 2110

Alfa AF: 0.142 Hom.: 5529

Bravo AF: 0.115

TwinsUK AF: 0.159 AC: 591

ALSPAC AF: 0.149 AC: 576

ESP6500AA AF: 0.0626 AC: 276

ESP6500EA AF: 0.156 AC: 1338

ExAC AF: 0.112 AC: 13560

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	2	not specified (2)
-	-	1	Familial temporal lobe epilepsy 5 (1)
-	-	1	Febrile seizures, familial, 11 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.063
BayesDel_addAF	Benign	-0.83	T
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.95
DEOGEN2	Benign	0.0036	T
Eigen	Benign	-0.38
Eigen_PC	Benign	-0.16
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Benign	0.20	T
MetaRNN	Benign	0.0019	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	-0.48	N
PhyloP100		1.1
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.25	N
REVEL	Benign	0.062
Sift	Benign	0.30	T
Sift4G	Benign	0.53	T
Polyphen		0.0010	B
Vest4		0.093
MPC		0.027
ClinPred		0.0025	T
GERP RS		4.1
Varity_R		0.037
gMVP		0.40
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.11
dbscSNV1_RF	Benign	0.19
SpliceAI score (max)		0.27		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.27		Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17343819; hg19: chr8-68396915; COSMIC: COSV107395807;