rs1866347

Variant names:

• chr8-23689997-G-A
• rs1866347
• XR_001745842.2:n.1312+21247G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-23689997-G-A
• chr8-23689997-G-C

Variant summary

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

The XR_001745842.2(LOC107986930):​n.1312+21247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,060 control chromosomes in the GnomAD database, including 6,978 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 0.28 (6978 hom., cov: 31)
• Consequence: LOC107986930 XR_001745842.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 3 publications found

Genes affected

LOC107986930 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42300 AN: 151942 Hom.: 6963 Cov.: 31

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.279 AC: 42368 AN: 152060 Hom.: 6978 Cov.: 31 AF XY: 0.277 AC XY: 20589 AN XY: 74324

African (AFR) AF: 0.451 AC: 18703 AN: 41448

American (AMR) AF: 0.263 AC: 4024 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3468

East Asian (EAS) AF: 0.0197 AC: 102 AN: 5180

South Asian (SAS) AF: 0.240 AC: 1160 AN: 4826

European-Finnish (FIN) AF: 0.243 AC: 2568 AN: 10554

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.213 AC: 14465 AN: 67978

Other (OTH) AF: 0.247 AC: 522 AN: 2110

Alfa AF: 0.220 Hom.: 12600

Bravo AF: 0.285

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.35
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1866347; hg19: chr8-23547510;