rs3102735

Positions:

• chr8-118952831-T-C

Variant summary

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

The NM_001324095.2(COLEC10):​c.-324+453T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,208 control chromosomes in the GnomAD database, including 2,129 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 0.16 (2129 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

Genes affected

COLEC10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COLEC10	NM_001324095.2	c.-324+453T>C		intron_variant
COLEC10	XM_005250756.4	c.-60+453T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25068 AN: 152088 Hom.: 2121 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.165 AC: 25092 AN: 152208 Hom.: 2129 Cov.: 32 AF XY: 0.162 AC XY: 12086 AN XY: 74422

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.150

Alfa AF: 0.145 Hom.: 2150

Bravo AF: 0.172

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3102735; hg19: chr8-119965070;