rs699213

Variant names:

• chr10-90210931-C-G
• rs699213
• ENST00000664430.1:n.696-14108C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-90210931-C-G
• chr10-90210931-C-T

Variant summary

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

The ENST00000664430.1(LINC00865):​n.696-14108C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,906 control chromosomes in the GnomAD database, including 8,750 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 0.32 (8750 hom., cov: 32)
• Consequence: LINC00865 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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.696-14108C>G		intron	N/A
	LINC00865	ENST00000749373.1		n.451-14108C>G		intron	N/A
	ENSG00000297645	ENST00000749546.1		n.290-30790G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48963 AN: 151788 Hom.: 8747 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.323 AC: 48992 AN: 151906 Hom.: 8750 Cov.: 32 AF XY: 0.324 AC XY: 24055 AN XY: 74212

African (AFR) AF: 0.474 AC: 19622 AN: 41418

American (AMR) AF: 0.267 AC: 4072 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 713 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2432 AN: 5130

South Asian (SAS) AF: 0.316 AC: 1523 AN: 4814

European-Finnish (FIN) AF: 0.270 AC: 2857 AN: 10564

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16758 AN: 67952

Other (OTH) AF: 0.308 AC: 650 AN: 2108

Alfa AF: 0.289 Hom.: 843

Bravo AF: 0.328

Asia WGS AF: 0.370 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.63
PhyloP100		0.41

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: rs699213;

hg19: chr10-91970688;