ENST00000658096.1:n.696-8853T>C

Variant names:

• chr17-43365383-A-G
• rs11657004
• ENST00000658096.1:n.696-8853T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658096.1(LINC00910):​n.696-8853T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,996 control chromosomes in the GnomAD database, including 14,941 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 0.43 (14941 hom., cov: 32)
• Consequence: LINC00910 ENST00000658096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.596 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.696-8853T>C		intron_variant	Intron 4 of 6
LINC00910	ENST00000661340.1	n.708+12288T>C		intron_variant	Intron 4 of 4
LINC00910	ENST00000662750.1	n.708+12288T>C		intron_variant	Intron 4 of 4
LINC00910	ENST00000664824.1	n.695+12288T>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64857 AN: 151878 Hom.: 14896 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.427 AC: 64947 AN: 151996 Hom.: 14941 Cov.: 32 AF XY: 0.431 AC XY: 32020 AN XY: 74304

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.419

Alfa AF: 0.370 Hom.: 5135

Bravo AF: 0.427

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.51
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11657004; hg19: chr17-41442751;