rs6986858

Variant names:

• chr8-115915834-C-T
• rs6986858
• XR_001745736.2:n.2344C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001745736.2(LOC107986902):​n.2344C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 151,782 control chromosomes in the GnomAD database, including 2,465 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 0.14 (2465 hom., cov: 32)
• Consequence: LOC107986902 XR_001745736.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 3 publications found

Genes affected

LOC107986902 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21799 AN: 151664 Hom.: 2455 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.0566

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0260

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.144 AC: 21835 AN: 151782 Hom.: 2465 Cov.: 32 AF XY: 0.148 AC XY: 10948 AN XY: 74146

African (AFR) AF: 0.267 AC: 11067 AN: 41382

American (AMR) AF: 0.290 AC: 4412 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0566 AC: 196 AN: 3464

East Asian (EAS) AF: 0.114 AC: 588 AN: 5156

South Asian (SAS) AF: 0.162 AC: 778 AN: 4794

European-Finnish (FIN) AF: 0.0260 AC: 274 AN: 10520

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0596 AC: 4048 AN: 67932

Other (OTH) AF: 0.132 AC: 278 AN: 2102

Alfa AF: 0.110 Hom.: 200

Bravo AF: 0.167

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.64
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs6986858; hg19: chr8-116928059;