chr8-126176894-T-C

Position:

• chr8-126176894-T-C

Variant summary

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

The ENST00000651482.1(LINC00861):​n.199-63813A>G 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 0.386 in 151,804 control chromosomes in the GnomAD database, including 12,521 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 0.39 (12521 hom., cov: 31)
• Consequence: LINC00861 ENST00000651482.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00861	ENST00000651482.1	n.199-63813A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58530 AN: 151686 Hom.: 12499 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.386 AC: 58606 AN: 151804 Hom.: 12521 Cov.: 31 AF XY: 0.384 AC XY: 28522 AN XY: 74190

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.352

Alfa AF: 0.306 Hom.: 11204

Bravo AF: 0.402

Asia WGS AF: 0.356 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7357357; hg19: chr8-127189138;