rs2292166

chr1-150912300-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.-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

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=-0.81).
• 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/exons	MANE	UniProt
CTXND2	NM_001384189.2	c.-15G>A		5_prime_UTR_variant	2/2	ENST00000636087.1
LOC107985204	XR_001738231.2	n.83-5209C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTXND2	ENST00000636087.1	c.-15G>A		5_prime_UTR_variant	2/2	2	NM_001384189.2	P1

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

Gnomad4 AFR exome AF: 0.0579

Gnomad4 AMR exome AF: 0.234

Gnomad4 ASJ exome AF: 0.144

Gnomad4 EAS exome AF: 0.187

Gnomad4 SAS exome AF: 0.209

Gnomad4 FIN exome AF: 0.263

Gnomad4 NFE exome AF: 0.253

Gnomad4 OTH exome AF: 0.229

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

Gnomad4 AFR AF: 0.0566

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.220

Alfa AF: 0.241 Hom.: 9358

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2292166; hg19: chr1-150884776;