rs7097398

Variant names:

• chr10-90051481-C-T
• rs7097398
• ENST00000664430.1:n.549-48811C>T

Variant summary

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

The ENST00000664430.1(LINC00865):​n.549-48811C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 152,264 control chromosomes in the GnomAD database, including 320 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 0.046 (320 hom., cov: 33)
• Consequence: LINC00865 ENST00000664430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 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.549-48811C>T		intron_variant	Intron 2 of 3
LINC00865	ENST00000749371.1	n.348-48811C>T		intron_variant	Intron 2 of 3
LINC00865	ENST00000749372.1	n.293-14667C>T		intron_variant	Intron 2 of 4
LINC00865	ENST00000749373.1	n.-203C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0458 AC: 6963 AN: 152146 Hom.: 320 Cov.: 33

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.0482

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0458 AC: 6974 AN: 152264 Hom.: 320 Cov.: 33 AF XY: 0.0498 AC XY: 3710 AN XY: 74450

African (AFR) AF: 0.0629 AC: 2614 AN: 41538

American (AMR) AF: 0.0971 AC: 1485 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3472

East Asian (EAS) AF: 0.181 AC: 936 AN: 5182

South Asian (SAS) AF: 0.0788 AC: 380 AN: 4822

European-Finnish (FIN) AF: 0.0482 AC: 511 AN: 10612

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0130 AC: 883 AN: 68038

Other (OTH) AF: 0.0422 AC: 89 AN: 2110

Alfa AF: 0.0245 Hom.: 249

Bravo AF: 0.0483

Asia WGS AF: 0.117 AC: 406 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.5
DANN	Benign	0.77
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7097398; hg19: chr10-91811238;