rs10466829

chr12-9723495-G-A

Variant summary

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

The NR_172485.1(CLECL1P):n.349-682C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 151,802 control chromosomes in the GnomAD database, including 23,409 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 0.55 (23409 hom., cov: 30)
• Consequence: CLECL1P NR_172485.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

CLECL1P (HGNC:24462): (C-type lectin like 1, pseudogene) This gene encodes a type II transmembrane, C-type lectin-like protein that is highly expressed on dendritic and B cells. This protein may act as a T-cell costimulatory molecule that enhances interleukin-4 production, and maybe involved in the regulation of the immune response. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLECL1P	NR_172485.1	n.349-682C>T		intron_variant, non_coding_transcript_variant
CLECL1P	NR_172486.1	n.349-682C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLECL1P	ENST00000327839.4	n.352-682C>T		intron_variant, non_coding_transcript_variant		1
CLECL1P	ENST00000621400.5	n.263-682C>T		intron_variant, non_coding_transcript_variant		5
CLECL1P	ENST00000702603.1	n.150-682C>T		intron_variant, non_coding_transcript_variant
CLECL1P	ENST00000542530.5	n.172-682C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83288 AN: 151682 Hom.: 23381 Cov.: 30

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.549 AC: 83360 AN: 151802 Hom.: 23409 Cov.: 30 AF XY: 0.551 AC XY: 40830 AN XY: 74162

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.529

Alfa AF: 0.511 Hom.: 26751

Bravo AF: 0.541

Asia WGS AF: 0.480 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.81
Dann	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10466829; hg19: chr12-9876091;