10-129801048-C-G

Variant names:

• chr10-129801048-C-G
• rs11016944
• ENST00000635764.2:n.752-546C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635764.2(LINC02666):​n.752-546C>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: LINC02666 ENST00000635764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 0 publications found

Genes affected

LINC02666 (HGNC:54152): (long intergenic non-protein coding RNA 2666)

LOC107984281 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635764.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC107984281	NR_186702.1		n.2511-546C>G		intron	N/A
	LOC107984281	NR_186705.1		n.7310-546C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02666	ENST00000635764.2	TSL:5	n.752-546C>G		intron	N/A

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

African (AFR) AF: 0.763 AC: 31639 AN: 41476

American (AMR) AF: 0.308 AC: 4716 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3470

East Asian (EAS) AF: 0.687 AC: 3534 AN: 5142

South Asian (SAS) AF: 0.359 AC: 1729 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2151 AN: 10570

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11576 AN: 67984

Other (OTH) AF: 0.349 AC: 737 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.33
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11016944; hg19: chr10-131599312;