chr8-115915475-G-A

Variant names:

• chr8-115915475-G-A
• rs6982767
• XR_001745736.2:n.1985G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745736.2(LOC107986902):​n.1985G>A 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 152,092 control chromosomes in the GnomAD database, including 2,477 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 (2477 hom., cov: 32)
• Consequence: LOC107986902 XR_001745736.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 4 publications found

Genes affected

LOC107986902 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 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: 21837 AN: 151974 Hom.: 2467 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.0563

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0981

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: 21873 AN: 152092 Hom.: 2477 Cov.: 32 AF XY: 0.148 AC XY: 10968 AN XY: 74354

African (AFR) AF: 0.267 AC: 11081 AN: 41456

American (AMR) AF: 0.289 AC: 4419 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0563 AC: 195 AN: 3464

East Asian (EAS) AF: 0.115 AC: 594 AN: 5164

South Asian (SAS) AF: 0.161 AC: 777 AN: 4816

European-Finnish (FIN) AF: 0.0263 AC: 279 AN: 10608

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0596 AC: 4054 AN: 67998

Other (OTH) AF: 0.132 AC: 279 AN: 2110

Alfa AF: 0.120 Hom.: 787

Bravo AF: 0.167

Asia WGS AF: 0.187 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	18
DANN	Benign	0.43
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6982767; hg19: chr8-116927700;