rs2292166

Variant names:

• chr1-150912300-G-A
• rs2292166
• NM_001384189.2:c.-15G>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.-15G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 398,390 control chromosomes in the GnomAD database, including 10,598 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 0.19 (3464 hom., cov: 32)
  • Exomes 𝑓: 0.23 (7134 hom.)
• Consequence: CTXND2 NM_001384189.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85
• Publications: 14 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]

ENSG00000295148 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTXND2	NM_001384189.2	c.-15G>A		5_prime_UTR_variant	Exon 2 of 2	ENST00000636087.1	NP_001371118.1
LOC107985204	XR_001738231.2	n.83-5209C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTXND2	ENST00000636087.1	c.-15G>A		5_prime_UTR_variant	Exon 2 of 2	2	NM_001384189.2	ENSP00000490418.1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29388 AN: 151986 Hom.: 3465 Cov.: 32

Gnomad AFR AF: 0.0565

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.222

GnomAD4 exome AF: 0.235 AC: 57815 AN: 246286 Hom.: 7134 Cov.: 0 AF XY: 0.235 AC XY: 29310 AN XY: 124798

African (AFR) AF: 0.0579 AC: 416 AN: 7180

American (AMR) AF: 0.234 AC: 1741 AN: 7434

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 1333 AN: 9240

East Asian (EAS) AF: 0.187 AC: 4282 AN: 22890

South Asian (SAS) AF: 0.209 AC: 631 AN: 3026

European-Finnish (FIN) AF: 0.263 AC: 5468 AN: 20822

Middle Eastern (MID) AF: 0.205 AC: 265 AN: 1294

European-Non Finnish (NFE) AF: 0.253 AC: 39932 AN: 158032

Other (OTH) AF: 0.229 AC: 3747 AN: 16368

GnomAD4 genome AF: 0.193 AC: 29393 AN: 152104 Hom.: 3464 Cov.: 32 AF XY: 0.193 AC XY: 14377 AN XY: 74334

African (AFR) AF: 0.0566 AC: 2351 AN: 41518

American (AMR) AF: 0.225 AC: 3434 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1424 AN: 5192

South Asian (SAS) AF: 0.207 AC: 999 AN: 4826

European-Finnish (FIN) AF: 0.257 AC: 2707 AN: 10550

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17243 AN: 67980

Other (OTH) AF: 0.220 AC: 463 AN: 2108

Alfa AF: 0.231 Hom.: 13865

Bravo AF: 0.185

Asia WGS AF: 0.236 AC: 825 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.8
DANN	Benign	0.67
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs2292166; hg19: chr1-150884776;