rs3134069

chr8-118952749-A-Cchr8-118952749-A-G

Variant summary

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

The NM_001324095.2(COLEC10):c.-324+371A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0943 in 152,166 control chromosomes in the GnomAD database, including 849 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 0.094 (849 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343

Genes affected

COLEC10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COLEC10	NM_001324095.2	c.-324+371A>C		intron_variant
COLEC10	XM_005250756.4	c.-60+371A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0943 AC: 14332 AN: 152046 Hom.: 841 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.0695

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

GnomAD4 genome AF: 0.0943 AC: 14348 AN: 152166 Hom.: 849 Cov.: 32 AF XY: 0.0928 AC XY: 6905 AN XY: 74384

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0380

Gnomad4 FIN AF: 0.0382

Gnomad4 NFE AF: 0.0560

Gnomad4 OTH AF: 0.0683

Alfa AF: 0.0404 Hom.: 51

Bravo AF: 0.105

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3134069; hg19: chr8-119964988;