rs986222

Variant names:

• chr10-90171130-G-A
• rs986222
• ENST00000664430.1:n.696-53909G>A

Variant summary

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

The ENST00000664430.1(LINC00865):​n.696-53909G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,984 control chromosomes in the GnomAD database, including 21,146 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 0.52 (21146 hom., cov: 32)
• Consequence: LINC00865 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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
LINC00865	ENST00000664430.1	n.696-53909G>A		intron_variant	Intron 3 of 3
LINC00865	ENST00000749371.1	n.495-2101G>A		intron_variant	Intron 3 of 3
LINC00865	ENST00000749373.1	n.451-53909G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78293 AN: 151866 Hom.: 21123 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.516 AC: 78355 AN: 151984 Hom.: 21146 Cov.: 32 AF XY: 0.527 AC XY: 39150 AN XY: 74280

African (AFR) AF: 0.507 AC: 21031 AN: 41452

American (AMR) AF: 0.547 AC: 8351 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2111 AN: 3466

East Asian (EAS) AF: 0.962 AC: 4974 AN: 5170

South Asian (SAS) AF: 0.745 AC: 3590 AN: 4816

European-Finnish (FIN) AF: 0.538 AC: 5686 AN: 10560

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31037 AN: 67940

Other (OTH) AF: 0.518 AC: 1092 AN: 2108

Alfa AF: 0.484 Hom.: 70740

Bravo AF: 0.512

Asia WGS AF: 0.826 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.14
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs986222; hg19: chr10-91930887;