rs7357357

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651482.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00861	ENST00000651482.1		n.199-63813A>G		intron	N/A

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

African (AFR) AF: 0.585 AC: 24195 AN: 41352

American (AMR) AF: 0.385 AC: 5868 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3466

East Asian (EAS) AF: 0.357 AC: 1835 AN: 5140

South Asian (SAS) AF: 0.295 AC: 1417 AN: 4802

European-Finnish (FIN) AF: 0.322 AC: 3401 AN: 10558

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19837 AN: 67926

Other (OTH) AF: 0.352 AC: 744 AN: 2114

Alfa AF: 0.325 Hom.: 18957

Bravo AF: 0.402

Asia WGS AF: 0.356 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.54
PhyloP100		0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7357357;

hg19: chr8-127189138;