rs4424296

chr8-119001037-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.-323-36399C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,990 control chromosomes in the GnomAD database, including 29,163 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 0.61 (29163 hom., cov: 32)
• Consequence: COLEC10 NM_001324095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468

Genes affected

COLEC10 (HGNC:2220): (collectin subfamily member 10) This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. The other members of this family are secreted proteins and bind to carbohydrate antigens on microorganisms facilitating their recognition and removal. This gene product is a cytosolic protein, a characteristic that suggests that it may have different biological functions than other C-lectins. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COLEC10	NM_001324095.2	c.-323-36399C>T		intron_variant
COLEC10	XM_005250756.4	c.-60+48659C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COLEC10	ENST00000521788.1	n.122+5464C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92000 AN: 151872 Hom.: 29123 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.606 AC: 92089 AN: 151990 Hom.: 29163 Cov.: 32 AF XY: 0.608 AC XY: 45195 AN XY: 74286

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.613

Alfa AF: 0.586 Hom.: 3877

Bravo AF: 0.611

Asia WGS AF: 0.649 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.0
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4424296; hg19: chr8-120013276;