chr10-83663098-G-T

Variant names:

• chr10-83663098-G-T
• rs2224865
• ENST00000791248.1:n.371+10041C>A

Variant summary

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

The ENST00000791248.1(LINC02650):​n.371+10041C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,152 control chromosomes in the GnomAD database, including 32,076 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 0.65 (32076 hom., cov: 33)
• Consequence: LINC02650 ENST00000791248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 12 publications found

Genes affected

LINC02650 (HGNC:54135): (long intergenic non-protein coding RNA 2650)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791248.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02650	ENST00000791248.1		n.371+10041C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98275 AN: 152032 Hom.: 32048 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.646 AC: 98362 AN: 152152 Hom.: 32076 Cov.: 33 AF XY: 0.647 AC XY: 48109 AN XY: 74396

African (AFR) AF: 0.596 AC: 24734 AN: 41502

American (AMR) AF: 0.784 AC: 11991 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2550 AN: 3472

East Asian (EAS) AF: 0.588 AC: 3041 AN: 5176

South Asian (SAS) AF: 0.624 AC: 3013 AN: 4830

European-Finnish (FIN) AF: 0.629 AC: 6656 AN: 10590

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44163 AN: 67976

Other (OTH) AF: 0.676 AC: 1424 AN: 2108

Alfa AF: 0.649 Hom.: 109191

Bravo AF: 0.661

Asia WGS AF: 0.639 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.28
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2224865; hg19: chr10-85422854;