chr20-55805499-C-T

Variant names:

• chr20-55805499-C-T
• rs6024437
• XR_936887.2:n.83+1517C>T

Variant summary

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

The XR_936887.2(LOC105372677):​n.83+1517C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,106 control chromosomes in the GnomAD database, including 6,525 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 0.27 (6525 hom., cov: 33)
• Consequence: LOC105372677 XR_936887.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 5 publications found

Genes affected

LOC105372677 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 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: 0.265 AC: 40313 AN: 151988 Hom.: 6513 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.265 AC: 40350 AN: 152106 Hom.: 6525 Cov.: 33 AF XY: 0.264 AC XY: 19599 AN XY: 74352

African (AFR) AF: 0.455 AC: 18880 AN: 41494

American (AMR) AF: 0.178 AC: 2710 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1004 AN: 3472

East Asian (EAS) AF: 0.138 AC: 712 AN: 5172

South Asian (SAS) AF: 0.227 AC: 1094 AN: 4828

European-Finnish (FIN) AF: 0.190 AC: 2010 AN: 10586

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13151 AN: 67968

Other (OTH) AF: 0.250 AC: 529 AN: 2116

Alfa AF: 0.214 Hom.: 16571

Bravo AF: 0.271

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	16
DANN	Benign	0.58
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs6024437; hg19: chr20-54380555;