rs2046159

Variant names:

• chr1-85864906-A-G
• rs2046159
• NM_152890.7:c.3300+3613T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152890.7(COL24A1):​c.3300+3613T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,184 control chromosomes in the GnomAD database, including 1,430 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 0.13 (1430 hom., cov: 32)
• Consequence: COL24A1 NM_152890.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.832
• Publications: 5 publications found

Genes affected

COL24A1 (HGNC:20821): (collagen type XXIV alpha 1 chain) This gene is a member of the collagen gene family and is thought to regulate type I collagen fibrillogenesis during fetal development. [provided by RefSeq, Mar 2017]

COL24A1 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152890.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL24A1	NM_152890.7	MANE Select	c.3300+3613T>C		intron	N/A	NP_690850.2
	COL24A1	NM_001349955.1		c.1200+3613T>C		intron	N/A	NP_001336884.1
	COL24A1	NR_146340.2		n.3493+3613T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL24A1	ENST00000370571.7	TSL:1 MANE Select	c.3300+3613T>C		intron	N/A	ENSP00000359603.2
	COL24A1	ENST00000426639.5	TSL:5	n.*750+3613T>C		intron	N/A	ENSP00000409515.1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19847 AN: 152066 Hom.: 1429 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00290

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.130 AC: 19849 AN: 152184 Hom.: 1430 Cov.: 32 AF XY: 0.127 AC XY: 9416 AN XY: 74416

African (AFR) AF: 0.103 AC: 4262 AN: 41536

American (AMR) AF: 0.116 AC: 1767 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3464

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5168

South Asian (SAS) AF: 0.165 AC: 797 AN: 4828

European-Finnish (FIN) AF: 0.0990 AC: 1049 AN: 10598

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11176 AN: 67996

Other (OTH) AF: 0.112 AC: 237 AN: 2110

Alfa AF: 0.157 Hom.: 1362

Bravo AF: 0.127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.85
PhyloP100		0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2046159; hg19: chr1-86330589;