1-85905466-T-C

Position:

• chr1-85905466-T-C

Variant summary

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

The NM_152890.7(COL24A1):​c.2778+1728A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,910 control chromosomes in the GnomAD database, including 8,464 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 0.31 (8464 hom., cov: 31)
• Consequence: COL24A1 NM_152890.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL24A1	NM_152890.7	c.2778+1728A>G		intron_variant		ENST00000370571.7	NP_690850.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL24A1	ENST00000370571.7	c.2778+1728A>G		intron_variant		1	NM_152890.7	ENSP00000359603.2
COL24A1	ENST00000426639.5	n.*228+1728A>G		intron_variant		5		ENSP00000409515.1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47578 AN: 151790 Hom.: 8457 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.313 AC: 47596 AN: 151910 Hom.: 8464 Cov.: 31 AF XY: 0.322 AC XY: 23919 AN XY: 74250

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.321

Alfa AF: 0.336 Hom.: 1573

Bravo AF: 0.308

Asia WGS AF: 0.398 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.9
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1858556; hg19: chr1-86371149;