10-90615069-T-G

Variant names:

• chr10-90615069-T-G
• rs1547851
• ENST00000660339.1:n.83+13701A>C

Variant summary

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

The ENST00000660339.1(LINC02653):​n.83+13701A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 152,196 control chromosomes in the GnomAD database, including 68,629 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 0.95 (68629 hom., cov: 31)
• Consequence: LINC02653 ENST00000660339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

Genes affected

LINC02653 (HGNC:54138): (long intergenic non-protein coding RNA 2653)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02653	ENST00000660339.1	n.83+13701A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.949 AC: 144329 AN: 152078 Hom.: 68568 Cov.: 31

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.949 AC: 144449 AN: 152196 Hom.: 68629 Cov.: 31 AF XY: 0.948 AC XY: 70521 AN XY: 74384

Gnomad4 AFR AF: 0.987

Gnomad4 AMR AF: 0.964

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.982

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.961

Alfa AF: 0.939 Hom.: 28154

Bravo AF: 0.958

Asia WGS AF: 0.990 AC: 3442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547851; hg19: chr10-92374826;