rs1564861

Positions:

• chr8-118953670-A-C
• chr8-118953670-A-G
• chr8-118953670-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+1292A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,006 control chromosomes in the GnomAD database, including 14,243 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 0.43 (14243 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

Genes affected

COLEC10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COLEC10	NM_001324095.2	c.-324+1292A>C		intron_variant			NP_001311024.1
COLEC10	XM_005250756.4	c.-60+1292A>C		intron_variant			XP_005250813.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64878 AN: 151888 Hom.: 14215 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.427 AC: 64941 AN: 152006 Hom.: 14243 Cov.: 32 AF XY: 0.431 AC XY: 32009 AN XY: 74284

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.443

Alfa AF: 0.412 Hom.: 2325

Bravo AF: 0.425

Asia WGS AF: 0.488 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564861; hg19: chr8-119965909;