rs248707

Positions:

• chr5-127658230-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001048252.3(CTXN3):​c.*463T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 174,066 control chromosomes in the GnomAD database, including 9,800 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.31 (8359 hom., cov: 32)
  • Exomes 𝑓: 0.35 (1441 hom.)
• Consequence: CTXN3 NM_001048252.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

CTXN3 (HGNC:31110): (cortexin 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTXN3	NM_001048252.3	c.*463T>C		3_prime_UTR_variant	3/3	ENST00000379445.8	NP_001041717.1
LOC105379164	XR_002956226.1	n.139+5394A>G		intron_variant, non_coding_transcript_variant
CTXN3	NM_001127385.2	c.*463T>C		3_prime_UTR_variant	3/3		NP_001120857.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTXN3	ENST00000379445.8	c.*463T>C		3_prime_UTR_variant	3/3	1	NM_001048252.3	ENSP00000368758	P1
CTXN3	ENST00000395322.3	c.*463T>C		3_prime_UTR_variant	3/3	1		ENSP00000378732	P1
	ENST00000512352.1	n.309+5394A>G		intron_variant, non_coding_transcript_variant		5
CTXN3	ENST00000620385.1	c.*463T>C		3_prime_UTR_variant	1/1			ENSP00000482081	P1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47752 AN: 151988 Hom.: 8357 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.341

GnomAD4 exome AF: 0.346 AC: 7592 AN: 21960 Hom.: 1441 Cov.: 0 AF XY: 0.343 AC XY: 3736 AN XY: 10878

Gnomad4 AFR exome AF: 0.150

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.297

Gnomad4 EAS exome AF: 0.228

Gnomad4 SAS exome AF: 0.270

Gnomad4 FIN exome AF: 0.349

Gnomad4 NFE exome AF: 0.385

Gnomad4 OTH exome AF: 0.382

GnomAD4 genome AF: 0.314 AC: 47753 AN: 152106 Hom.: 8359 Cov.: 32 AF XY: 0.308 AC XY: 22909 AN XY: 74342

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.336

Alfa AF: 0.338 Hom.: 4716

Bravo AF: 0.302

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.8
DANN	Benign	0.72

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: rs248707; hg19: chr5-126993922; COSMIC: COSV65218459; COSMIC: COSV65218459;