rs1865997

chr15-80199111-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001352888.2(CTXND1):c.*2659A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,054 control chromosomes in the GnomAD database, including 13,835 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 0.42 (13832 hom., cov: 32)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: CTXND1 NM_001352888.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922

Genes affected

CTXND1 (HGNC:50507): (cortexin domain containing 1) 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTXND1	NM_001352888.2	c.*2659A>G		3_prime_UTR_variant	3/3	ENST00000560778.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTXND1	ENST00000560778.3	c.*2659A>G		3_prime_UTR_variant	3/3	3	NM_001352888.2	P1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64531 AN: 151930 Hom.: 13825 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.426

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.425 AC: 64579 AN: 152048 Hom.: 13832 Cov.: 32 AF XY: 0.425 AC XY: 31598 AN XY: 74330

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.425

Alfa AF: 0.402 Hom.: 25428

Bravo AF: 0.415

Asia WGS AF: 0.418 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.71
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1865997; hg19: chr15-80491453;