rs12410394

Variant names:

• chr1-150887710-G-A
• rs12410394
• NM_001384189.2:c.-74+397G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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]

ENSG00000295171 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CTXND2	NM_001384189.2	c.-74+397G>A		intron_variant	Intron 1 of 1	ENST00000636087.1	NP_001371118.1
LOC107985204	XR_007066618.1	n.437C>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+397G>A		intron_variant	Intron 1 of 1	2	NM_001384189.2	ENSP00000490418.1
ENSG00000295171	ENST00000728455.1	n.671C>T		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000295148	ENST00000728253.1	n.86-6005C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.281 AC: 11623 AN: 41404

American (AMR) AF: 0.471 AC: 7170 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1483 AN: 3472

East Asian (EAS) AF: 0.446 AC: 2304 AN: 5164

South Asian (SAS) AF: 0.536 AC: 2580 AN: 4814

European-Finnish (FIN) AF: 0.346 AC: 3646 AN: 10542

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24069 AN: 67946

Other (OTH) AF: 0.364 AC: 766 AN: 2102

Alfa AF: 0.357 Hom.: 16615

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs12410394; hg19: chr1-150860186;