chr20-55820485-A-G

Variant names:

• chr20-55820485-A-G
• rs6024460
• XR_936887.2:n.84-6274A>G

Variant summary

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

The XR_936887.2(LOC105372677):​n.84-6274A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,934 control chromosomes in the GnomAD database, including 5,174 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 0.24 (5174 hom., cov: 31)
• Consequence: LOC105372677 XR_936887.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 4 publications found

Genes affected

LOC105372677 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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: 0.244 AC: 36973 AN: 151816 Hom.: 5163 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.244 AC: 37002 AN: 151934 Hom.: 5174 Cov.: 31 AF XY: 0.243 AC XY: 18042 AN XY: 74278

African (AFR) AF: 0.382 AC: 15826 AN: 41398

American (AMR) AF: 0.168 AC: 2566 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1009 AN: 3470

East Asian (EAS) AF: 0.138 AC: 712 AN: 5158

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4812

European-Finnish (FIN) AF: 0.187 AC: 1970 AN: 10546

Middle Eastern (MID) AF: 0.331 AC: 96 AN: 290

European-Non Finnish (NFE) AF: 0.192 AC: 13064 AN: 67974

Other (OTH) AF: 0.240 AC: 506 AN: 2112

Alfa AF: 0.210 Hom.: 5893

Bravo AF: 0.246

Asia WGS AF: 0.194 AC: 671 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.025
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6024460; hg19: chr20-54395541;