5-127655764-G-C

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001048252.3(CTXN3):​c.-99-1659G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CTXN3 NM_001048252.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTXN3	NM_001048252.3	c.-99-1659G>C		intron_variant	Intron 2 of 2	ENST00000379445.8	NP_001041717.1
CTXN3	NM_001127385.2	c.-99-1659G>C		intron_variant	Intron 2 of 2		NP_001120857.1
LOC105379164	XR_002956226.1	n.140-3403C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTXN3	ENST00000379445.8	c.-99-1659G>C		intron_variant	Intron 2 of 2	1	NM_001048252.3	ENSP00000368758.3
CTXN3	ENST00000395322.3	c.-99-1659G>C		intron_variant	Intron 2 of 2	1		ENSP00000378732.3
ENSG00000248799	ENST00000512352.1	n.310-3403C>G		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.45

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: rs7711139; hg19: chr5-126991456;