5-127655764-G-A

Variant names:

• chr5-127655764-G-A
• rs7711139
• NM_001048252.3:c.-99-1659G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001048252.3(CTXN3):​c.-99-1659G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,964 control chromosomes in the GnomAD database, including 1,336 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 0.12 (1336 hom., cov: 32)
• Consequence: CTXN3 NM_001048252.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 3 publications found

Genes affected

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

ENSG00000248799 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001048252.3. 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
	CTXN3	NM_001048252.3	MANE Select	c.-99-1659G>A		intron	N/A	NP_001041717.1	Q4LDR2
	CTXN3	NM_001127385.2		c.-99-1659G>A		intron	N/A	NP_001120857.1	Q4LDR2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTXN3	ENST00000379445.8	TSL:1 MANE Select	c.-99-1659G>A		intron	N/A	ENSP00000368758.3	Q4LDR2
	CTXN3	ENST00000395322.3	TSL:1	c.-99-1659G>A		intron	N/A	ENSP00000378732.3	Q4LDR2
	ENSG00000248799	ENST00000512352.1	TSL:5	n.310-3403C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18219 AN: 151846 Hom.: 1335 Cov.: 32

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.125

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.120 AC: 18227 AN: 151964 Hom.: 1336 Cov.: 32 AF XY: 0.124 AC XY: 9240 AN XY: 74260

African (AFR) AF: 0.0974 AC: 4035 AN: 41418

American (AMR) AF: 0.184 AC: 2814 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3462

East Asian (EAS) AF: 0.292 AC: 1501 AN: 5148

South Asian (SAS) AF: 0.118 AC: 567 AN: 4810

European-Finnish (FIN) AF: 0.148 AC: 1564 AN: 10556

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6937 AN: 67980

Other (OTH) AF: 0.128 AC: 270 AN: 2112

Alfa AF: 0.107 Hom.: 1943

Bravo AF: 0.125

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.77
DANN	Benign	0.45
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

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: rs7711139; hg19: chr5-126991456;