chr10-90029031-T-G

Variant names:

• chr10-90029031-T-G
• rs11185978
• ENST00000664430.1:n.549-71261T>G

Variant summary

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

The ENST00000664430.1(LINC00865):​n.549-71261T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,208 control chromosomes in the GnomAD database, including 291 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 0.051 (291 hom., cov: 32)
• Consequence: LINC00865 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.091 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.549-71261T>G		intron_variant	Intron 2 of 3
LINC00865	ENST00000749371.1	n.348-71261T>G		intron_variant	Intron 2 of 3
LINC00865	ENST00000749372.1	n.293-37117T>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7730 AN: 152090 Hom.: 290 Cov.: 32

Gnomad AFR AF: 0.0935

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0509 AC: 7741 AN: 152208 Hom.: 291 Cov.: 32 AF XY: 0.0479 AC XY: 3569 AN XY: 74432

African (AFR) AF: 0.0935 AC: 3882 AN: 41538

American (AMR) AF: 0.0321 AC: 491 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3468

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5190

South Asian (SAS) AF: 0.0106 AC: 51 AN: 4816

European-Finnish (FIN) AF: 0.0123 AC: 130 AN: 10594

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

European-Non Finnish (NFE) AF: 0.0426 AC: 2899 AN: 68002

Other (OTH) AF: 0.0398 AC: 84 AN: 2110

Alfa AF: 0.0448 Hom.: 23

Bravo AF: 0.0542

Asia WGS AF: 0.0160 AC: 56 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.72
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs11185978; hg19: chr10-91788788;