chr1-150887995-C-T

Variant names:

• chr1-150887995-C-T
• rs7412746
• NM_001384189.2:c.-74+682C>T

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+682C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,564 control chromosomes in the GnomAD database, including 15,056 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 0.41 (15056 hom., cov: 30)
• Consequence: CTXND2 NM_001384189.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 81 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTXND2	NM_001384189.2	c.-74+682C>T		intron_variant	Intron 1 of 1	ENST00000636087.1	NP_001371118.1
LOC107985204	XR_007066618.1	n.152G>A		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+682C>T		intron_variant	Intron 1 of 1	2	NM_001384189.2	ENSP00000490418.1
ENSG00000295148	ENST00000728253.1	n.86-6290G>A		intron_variant	Intron 1 of 1
ENSG00000295171	ENST00000728455.1	n.537-151G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62119 AN: 151442 Hom.: 15056 Cov.: 30

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.410 AC: 62125 AN: 151564 Hom.: 15056 Cov.: 30 AF XY: 0.408 AC XY: 30202 AN XY: 74046

African (AFR) AF: 0.172 AC: 7135 AN: 41386

American (AMR) AF: 0.383 AC: 5816 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1385 AN: 3454

East Asian (EAS) AF: 0.370 AC: 1912 AN: 5166

South Asian (SAS) AF: 0.319 AC: 1525 AN: 4788

European-Finnish (FIN) AF: 0.561 AC: 5896 AN: 10512

Middle Eastern (MID) AF: 0.438 AC: 127 AN: 290

European-Non Finnish (NFE) AF: 0.544 AC: 36865 AN: 67794

Other (OTH) AF: 0.436 AC: 914 AN: 2098

Alfa AF: 0.494 Hom.: 79151

Bravo AF: 0.387

Asia WGS AF: 0.359 AC: 1253 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.29
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7412746; hg19: chr1-150860471;