rs1112578

Positions:

• chr2-189390032-G-A
• chr2-189390032-G-C

Variant summary

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

The XM_011510573.4(COL5A2):​c.-331+39260C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,856 control chromosomes in the GnomAD database, including 26,077 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 0.57 (26077 hom., cov: 31)
• Consequence: COL5A2 XM_011510573.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

COL5A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL5A2	XM_011510573.4	c.-331+39260C>T		intron_variant			XP_011508875.1
COL5A2	XM_047443251.1	c.-502-391C>T		intron_variant			XP_047299207.1
COL5A2	XM_047443252.1	c.-455-41836C>T		intron_variant			XP_047299208.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85837 AN: 151738 Hom.: 26064 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.566 AC: 85888 AN: 151856 Hom.: 26077 Cov.: 31 AF XY: 0.566 AC XY: 41983 AN XY: 74206

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.593

Alfa AF: 0.645 Hom.: 17011

Bravo AF: 0.549

Asia WGS AF: 0.600 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1112578; hg19: chr2-190254758;