rs12410394

chr1-150887710-G-A

Variant summary

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

The NM_001384189.2(CTXND2):c.-74+397G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,870 control chromosomes in the GnomAD database, including 9,998 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 0.36 (9998 hom., cov: 31)
• Consequence: CTXND2 NM_001384189.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTXND2	NM_001384189.2	c.-74+397G>A		intron_variant		ENST00000636087.1
LOC107985204	XR_007066618.1	n.437C>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTXND2	ENST00000636087.1	c.-74+397G>A		intron_variant		2	NM_001384189.2	P1

Frequencies

GnomAD3 genomes AF: 0.356 AC: 53983 AN: 151752 Hom.: 9988 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.356 AC: 53998 AN: 151870 Hom.: 9998 Cov.: 31 AF XY: 0.362 AC XY: 26845 AN XY: 74222

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.364

Alfa AF: 0.353 Hom.: 1650

Bravo AF: 0.360

Asia WGS AF: 0.443 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.2
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12410394; hg19: chr1-150860186;