rs2046159

chr1-85864906-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL24A1	NM_152890.7	c.3300+3613T>C		intron_variant		ENST00000370571.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL24A1	ENST00000370571.7	c.3300+3613T>C		intron_variant		1	NM_152890.7	P1
COL24A1	ENST00000426639.5	c.*750+3613T>C		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.112

Alfa AF: 0.157 Hom.: 1247

Bravo AF: 0.127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	16
Dann	Benign	0.85

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046159; hg19: chr1-86330589;