rs12679857

chr8-118965098-A-Gchr8-118965098-A-T

Variant summary

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

The NM_001324095.2(COLEC10):c.-324+12720A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,024 control chromosomes in the GnomAD database, including 10,233 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 0.36 (10233 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

COLEC10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COLEC10	NM_001324095.2	c.-324+12720A>G		intron_variant
COLEC10	XM_005250756.4	c.-60+12720A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54397 AN: 151906 Hom.: 10226 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.358 AC: 54428 AN: 152024 Hom.: 10233 Cov.: 32 AF XY: 0.364 AC XY: 27057 AN XY: 74312

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.345

Alfa AF: 0.309 Hom.: 9173

Bravo AF: 0.352

Asia WGS AF: 0.471 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.3
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12679857; hg19: chr8-119977337;