chr10-90058530-A-G

Variant names:

• chr10-90058530-A-G
• rs7071717
• ENST00000664430.1:n.549-41762A>G

Variant summary

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

The ENST00000664430.1(LINC00865):​n.549-41762A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 152,272 control chromosomes in the GnomAD database, including 446 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 0.061 (446 hom., cov: 33)
• Consequence: LINC00865 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 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.549-41762A>G		intron_variant	Intron 2 of 3
LINC00865	ENST00000749371.1	n.348-41762A>G		intron_variant	Intron 2 of 3
LINC00865	ENST00000749372.1	n.293-7618A>G		intron_variant	Intron 2 of 4
LINC00865	ENST00000749373.1	n.99+6748A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9254 AN: 152154 Hom.: 442 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0364

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0443

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0609 AC: 9267 AN: 152272 Hom.: 446 Cov.: 33 AF XY: 0.0579 AC XY: 4314 AN XY: 74470

African (AFR) AF: 0.125 AC: 5172 AN: 41542

American (AMR) AF: 0.0364 AC: 556 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3472

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5184

South Asian (SAS) AF: 0.0270 AC: 130 AN: 4822

European-Finnish (FIN) AF: 0.0127 AC: 135 AN: 10614

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0443 AC: 3016 AN: 68024

Other (OTH) AF: 0.0497 AC: 105 AN: 2114

Alfa AF: 0.0522 Hom.: 41

Bravo AF: 0.0650

Asia WGS AF: 0.0290 AC: 103 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.67
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7071717; hg19: chr10-91818287;