10-129801048-C-G

Position:

• chr10-129801048-C-G

Variant summary

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

The NR_186702.1(LOC107984281):​n.2511-546C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,070 control chromosomes in the GnomAD database, including 15,946 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 0.38 (15946 hom., cov: 33)
• Consequence: LOC107984281 NR_186702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

Genes affected

LINC02666 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984281	NR_186702.1	n.2511-546C>G		intron_variant
LOC107984281	NR_186705.1	n.7310-546C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02666	ENST00000635764.1	n.638-546C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57076 AN: 151952 Hom.: 15897 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.376 AC: 57178 AN: 152070 Hom.: 15946 Cov.: 33 AF XY: 0.378 AC XY: 28059 AN XY: 74328

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.349

Alfa AF: 0.100 Hom.: 147

Bravo AF: 0.406

Asia WGS AF: 0.497 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11016944; hg19: chr10-131599312;