rs7092929

Positions:

• chr10-3496602-A-C
• chr10-3496602-A-T

Variant summary

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

The NR_155744.1(LINC02669):​n.632-4T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 151,926 control chromosomes in the GnomAD database, including 45,196 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 0.76 (45196 hom., cov: 31)
• Consequence: LINC02669 NR_155744.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

Genes affected

LINC02669 (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 (NFE) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.162+177746A>C		intron_variant
LINC02669	NR_155743.1	n.631+1051T>G		intron_variant
LINC02669	NR_155744.1	n.632-4T>G		splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02669	ENST00000413993.2	n.709-366T>G		intron_variant		3
LINC02669	ENST00000655104.1	n.413+1051T>G		intron_variant
LINC02669	ENST00000656403.1	n.548-4T>G		splice_region_variant, intron_variant

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116137 AN: 151808 Hom.: 45183 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.765 AC: 116195 AN: 151926 Hom.: 45196 Cov.: 31 AF XY: 0.755 AC XY: 56108 AN XY: 74272

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.785

Alfa AF: 0.806 Hom.: 19434

Bravo AF: 0.761

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7092929; hg19: chr10-3538794;