ENST00000658096.1:n.696-2285T>C

Variant names:

• chr17-43358815-A-G
• rs4793234
• ENST00000658096.1:n.696-2285T>C

Variant summary

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

The ENST00000658096.1(LINC00910):​n.696-2285T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,026 control chromosomes in the GnomAD database, including 8,084 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 (8084 hom., cov: 32)
• Consequence: LINC00910 ENST00000658096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 12 publications found

Genes affected

LINC00910 (HGNC:44361): (long intergenic non-protein coding RNA 910)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 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
LINC00910	ENST00000658096.1	n.696-2285T>C		intron_variant	Intron 4 of 6
LINC00910	ENST00000661340.1	n.709-9486T>C		intron_variant	Intron 4 of 4
LINC00910	ENST00000662750.1	n.709-17356T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48486 AN: 151916 Hom.: 8079 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.319 AC: 48512 AN: 152026 Hom.: 8084 Cov.: 32 AF XY: 0.326 AC XY: 24205 AN XY: 74324

African (AFR) AF: 0.235 AC: 9716 AN: 41362

American (AMR) AF: 0.331 AC: 5059 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1917 AN: 5180

South Asian (SAS) AF: 0.494 AC: 2387 AN: 4828

European-Finnish (FIN) AF: 0.404 AC: 4282 AN: 10588

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22821 AN: 67996

Other (OTH) AF: 0.339 AC: 716 AN: 2114

Alfa AF: 0.340 Hom.: 4516

Bravo AF: 0.305

Asia WGS AF: 0.417 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4793234; hg19: chr17-41436183;