10-90615069-T-G

Variant names:

• chr10-90615069-T-G
• rs1547851
• ENST00000660339.2:n.212+13701A>C

Variant summary

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

The ENST00000660339.2(LINC02653):​n.212+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 ENST00000660339.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660339.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02653	ENST00000660339.2		n.212+13701A>C		intron	N/A

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

African (AFR) AF: 0.987 AC: 41025 AN: 41564

American (AMR) AF: 0.964 AC: 14725 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3299 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5151 AN: 5154

South Asian (SAS) AF: 0.982 AC: 4736 AN: 4822

European-Finnish (FIN) AF: 0.864 AC: 9154 AN: 10592

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63233 AN: 68002

Other (OTH) AF: 0.961 AC: 2028 AN: 2110

Alfa AF: 0.948 Hom.: 49362

Bravo AF: 0.958

Asia WGS AF: 0.990 AC: 3442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.43
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1547851; hg19: chr10-92374826;