8-20842529-C-G

Variant names:

• chr8-20842529-C-G
• rs2927385
• XR_949569.4:n.182+51973C>G

Variant summary

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

The XR_949569.4(LOC105379315):​n.182+51973C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,998 control chromosomes in the GnomAD database, including 33,509 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 0.65 (33509 hom., cov: 31)
• Consequence: LOC105379315 XR_949569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 5 publications found

Genes affected

LOC105379315 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 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: 0.646 AC: 98074 AN: 151880 Hom.: 33455 Cov.: 31

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.646 AC: 98181 AN: 151998 Hom.: 33509 Cov.: 31 AF XY: 0.638 AC XY: 47397 AN XY: 74270

African (AFR) AF: 0.864 AC: 35861 AN: 41492

American (AMR) AF: 0.602 AC: 9186 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1973 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1222 AN: 5160

South Asian (SAS) AF: 0.616 AC: 2965 AN: 4810

European-Finnish (FIN) AF: 0.500 AC: 5253 AN: 10512

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39816 AN: 67970

Other (OTH) AF: 0.628 AC: 1326 AN: 2110

Alfa AF: 0.410 Hom.: 796

Bravo AF: 0.659

Asia WGS AF: 0.490 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.35
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2927385; hg19: chr8-20700040;