chr1-85815462-C-A

Variant names:

• chr1-85815462-C-A
• rs313757
• NM_152890.7:c.3951+1326G>T

Variant summary

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

The NM_152890.7(COL24A1):​c.3951+1326G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,856 control chromosomes in the GnomAD database, including 16,408 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 0.46 (16408 hom., cov: 32)
• Consequence: COL24A1 NM_152890.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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.3951+1326G>T		intron	N/A	NP_690850.2	Q17RW2-1
	COL24A1	NM_001349955.1		c.1851+1326G>T		intron	N/A	NP_001336884.1
	COL24A1	NR_146340.2		n.4136+1326G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL24A1	ENST00000370571.7	TSL:1 MANE Select	c.3951+1326G>T		intron	N/A	ENSP00000359603.2	Q17RW2-1
	COL24A1	ENST00000426639.5	TSL:5	n.*1401+1326G>T		intron	N/A	ENSP00000409515.1	F8WDM8

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69912 AN: 151738 Hom.: 16400 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.461 AC: 69954 AN: 151856 Hom.: 16408 Cov.: 32 AF XY: 0.466 AC XY: 34579 AN XY: 74232

African (AFR) AF: 0.460 AC: 19029 AN: 41404

American (AMR) AF: 0.409 AC: 6245 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3468

East Asian (EAS) AF: 0.582 AC: 3010 AN: 5168

South Asian (SAS) AF: 0.547 AC: 2631 AN: 4812

European-Finnish (FIN) AF: 0.512 AC: 5382 AN: 10520

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30508 AN: 67912

Other (OTH) AF: 0.475 AC: 1002 AN: 2110

Alfa AF: 0.337 Hom.: 937

Bravo AF: 0.455

Asia WGS AF: 0.548 AC: 1899 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.92
DANN	Benign	0.67
PhyloP100		-0.23
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: rs313757; hg19: chr1-86281145;