rs3134070

Positions:

• chr8-118952785-C-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+407C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 152,200 control chromosomes in the GnomAD database, including 850 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 (850 hom., cov: 33)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

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	Protein	UniProt
COLEC10	NM_001324095.2	c.-324+407C>T		intron_variant			NP_001311024.1
COLEC10	XM_005250756.4	c.-60+407C>T		intron_variant			XP_005250813.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0943 AC: 14346 AN: 152082 Hom.: 842 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0387

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.0693

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

GnomAD4 genome AF: 0.0944 AC: 14362 AN: 152200 Hom.: 850 Cov.: 33 AF XY: 0.0929 AC XY: 6913 AN XY: 74408

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0616

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0382

Gnomad4 FIN AF: 0.0382

Gnomad4 NFE AF: 0.0560

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0816 Hom.: 115

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	0.23
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3134070; hg19: chr8-119965024;