16-78058281-T-G

Position:

• chr16-78058281-T-G

Variant summary

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

The ENST00000563114.1(ENSG00000261540):​n.41+1133A>C 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 0.677 in 151,706 control chromosomes in the GnomAD database, including 35,448 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 0.68 (35448 hom., cov: 34)
• Consequence: ENST00000563114.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

CLEC3A (HGNC:2052): (C-type lectin domain family 3 member A) Predicted to enable carbohydrate binding activity. Predicted to be involved in ossification. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

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 = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984897	XR_001752267.2	n.354-5432T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC3A	ENST00000567430.2	c.*181+6132T>G		intron_variant, NMD_transcript_variant		1		ENSP00000457211
	ENST00000563114.1	n.41+1133A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102652 AN: 151588 Hom.: 35403 Cov.: 34

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.677 AC: 102752 AN: 151706 Hom.: 35448 Cov.: 34 AF XY: 0.677 AC XY: 50187 AN XY: 74122

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.618

Alfa AF: 0.632 Hom.: 40812

Bravo AF: 0.675

Asia WGS AF: 0.559 AC: 1946 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	3.3
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1922604; hg19: chr16-78092178;