rs10399947

chr1-150889484-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+2171G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,288 control chromosomes in the GnomAD database, including 15,221 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 0.43 (15221 hom., cov: 31)
• Consequence: CTXND2 NM_001384189.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTXND2	NM_001384189.2	c.-74+2171G>A		intron_variant		ENST00000636087.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTXND2	ENST00000636087.1	c.-74+2171G>A		intron_variant		2	NM_001384189.2	P1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65741 AN: 151186 Hom.: 15201 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.435 AC: 65798 AN: 151288 Hom.: 15221 Cov.: 31 AF XY: 0.439 AC XY: 32396 AN XY: 73830

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.427

Alfa AF: 0.382 Hom.: 19502

Bravo AF: 0.449

Asia WGS AF: 0.467 AC: 1619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.6
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10399947; hg19: chr1-150861960;