rs7357357

Variant names:

• chr8-126176894-T-C
• rs7357357
• ENST00000651482.1:n.199-63813A>G

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00861	ENST00000651482.1	n.199-63813A>G		intron_variant	Intron 1 of 3

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;