rs7412746

Variant names:

• chr1-150887995-C-A
• rs7412746
• NM_001384189.2:c.-74+682C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-150887995-C-A
• chr1-150887995-C-G
• chr1-150887995-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001384189.2(CTXND2):​c.-74+682C>A 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: 30)
• Consequence: CTXND2 NM_001384189.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 81 publications found

Genes affected

CTXND2 (HGNC:53440): (cortexin domain containing 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC107985204 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTXND2	NM_001384189.2	c.-74+682C>A		intron_variant	Intron 1 of 1	ENST00000636087.1	NP_001371118.1
LOC107985204	XR_007066618.1	n.152G>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTXND2	ENST00000636087.1	c.-74+682C>A		intron_variant	Intron 1 of 1	2	NM_001384189.2	ENSP00000490418.1
ENSG00000295148	ENST00000728253.1	n.86-6290G>T		intron_variant	Intron 1 of 1
ENSG00000295171	ENST00000728455.1	n.537-151G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 79151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7412746; hg19: chr1-150860471;