chr10-127880410-T-C

Position:

• chr10-127880410-T-C

Variant summary

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

The NM_152311.5(CLRN3):​c.410-1990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,012 control chromosomes in the GnomAD database, including 20,251 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 0.47 (20251 hom., cov: 31)
• Consequence: CLRN3 NM_152311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

CLRN3 (HGNC:20795): (clarin 3) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLRN3	NM_152311.5	c.410-1990A>G		intron_variant		ENST00000368671.4
CLRN3	XM_011539274.3	c.230-1990A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLRN3	ENST00000368671.4	c.410-1990A>G		intron_variant		1	NM_152311.5	P1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71423 AN: 151894 Hom.: 20246 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.470 AC: 71425 AN: 152012 Hom.: 20251 Cov.: 31 AF XY: 0.478 AC XY: 35521 AN XY: 74288

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.467

Alfa AF: 0.577 Hom.: 21156

Bravo AF: 0.440

Asia WGS AF: 0.428 AC: 1487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs6482992; hg19: chr10-129678674;