10-90202913-A-G

Variant names:

• chr10-90202913-A-G
• rs2250245
• ENST00000664430.1:n.696-22126A>G

Variant summary

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

The ENST00000664430.1(LINC00865):​n.696-22126A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,742 control chromosomes in the GnomAD database, including 9,134 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 0.33 (9134 hom., cov: 32)
• Consequence: LINC00865 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876
• Publications: 7 publications found

Genes affected

LINC00865 (HGNC:45170): (long intergenic non-protein coding RNA 865)

ENSG00000297645 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664430.1. 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
	LINC00865	ENST00000664430.1		n.696-22126A>G		intron	N/A
	LINC00865	ENST00000749373.1		n.451-22126A>G		intron	N/A
	ENSG00000297645	ENST00000749546.1		n.290-22772T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50032 AN: 151624 Hom.: 9132 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.330 AC: 50061 AN: 151742 Hom.: 9134 Cov.: 32 AF XY: 0.331 AC XY: 24556 AN XY: 74176

African (AFR) AF: 0.481 AC: 19934 AN: 41406

American (AMR) AF: 0.274 AC: 4170 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3466

East Asian (EAS) AF: 0.473 AC: 2430 AN: 5140

South Asian (SAS) AF: 0.326 AC: 1568 AN: 4812

European-Finnish (FIN) AF: 0.274 AC: 2902 AN: 10582

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17286 AN: 67804

Other (OTH) AF: 0.312 AC: 658 AN: 2106

Alfa AF: 0.279 Hom.: 17904

Bravo AF: 0.335

Asia WGS AF: 0.380 AC: 1324 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.48
PhyloP100		0.88

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2250245;

hg19: chr10-91962670;