rs1906493

Positions:

• chr8-126080638-G-T

Variant summary

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

The ENST00000651482.1(LINC00861):​n.366+28487C>A 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 0.132 in 152,122 control chromosomes in the GnomAD database, including 1,476 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 0.13 (1476 hom., cov: 32)
• Consequence: LINC00861 ENST00000651482.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 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.366+28487C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20052 AN: 152004 Hom.: 1479 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0628

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.132 AC: 20051 AN: 152122 Hom.: 1476 Cov.: 32 AF XY: 0.134 AC XY: 9946 AN XY: 74346

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0630

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.120

Alfa AF: 0.142 Hom.: 1514

Bravo AF: 0.123

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.43
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1906493; hg19: chr8-127092882;