rs10399947

Variant names:

• chr1-150889484-G-A
• rs10399947
• NM_001384189.2:c.-74+2171G>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+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
• Publications: 18 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]

LOC107985204 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384189.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTXND2	NM_001384189.2	MANE Select	c.-74+2171G>A		intron	N/A	NP_001371118.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTXND2	ENST00000636087.1	TSL:2 MANE Select	c.-74+2171G>A		intron	N/A	ENSP00000490418.1
	ENSG00000295148	ENST00000728253.1		n.86-7779C>T		intron	N/A
	ENSG00000295171	ENST00000728455.1		n.537-1640C>T		intron	N/A

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

African (AFR) AF: 0.544 AC: 22440 AN: 41248

American (AMR) AF: 0.502 AC: 7626 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1540 AN: 3456

East Asian (EAS) AF: 0.447 AC: 2308 AN: 5158

South Asian (SAS) AF: 0.543 AC: 2600 AN: 4784

European-Finnish (FIN) AF: 0.350 AC: 3639 AN: 10388

Middle Eastern (MID) AF: 0.421 AC: 122 AN: 290

European-Non Finnish (NFE) AF: 0.360 AC: 24389 AN: 67774

Other (OTH) AF: 0.427 AC: 891 AN: 2088

Alfa AF: 0.397 Hom.: 32885

Bravo AF: 0.449

Asia WGS AF: 0.467 AC: 1619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10399947; hg19: chr1-150861960;