rs4560755

chr8-126280511-G-A

Variant summary

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

The ENST00000651482.1(LINC00861):n.198+12080C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,006 control chromosomes in the GnomAD database, including 4,726 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 0.25 (4726 hom., cov: 32)
• Consequence: LINC00861 ENST00000651482.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382

Genes affected

LINC00861 (HGNC:45133): (long intergenic non-protein coding RNA 861)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00861	ENST00000651482.1	n.198+12080C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37237 AN: 151888 Hom.: 4724 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.245 AC: 37242 AN: 152006 Hom.: 4726 Cov.: 32 AF XY: 0.247 AC XY: 18321 AN XY: 74290

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.249

Alfa AF: 0.259 Hom.: 2510

Bravo AF: 0.235

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.74
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4560755; hg19: chr8-127292756;