rs6092179

Variant names:

• chr20-55803977-C-A
• rs6092179
• XR_936887.2:n.78C>A

Variant summary

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

The XR_936887.2(LOC105372677):​n.78C>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 0.212 in 151,738 control chromosomes in the GnomAD database, including 3,713 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 0.21 (3713 hom., cov: 32)
• Consequence: LOC105372677 XR_936887.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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: 0.212 AC: 32199 AN: 151620 Hom.: 3703 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.212 AC: 32231 AN: 151738 Hom.: 3713 Cov.: 32 AF XY: 0.212 AC XY: 15722 AN XY: 74122

African (AFR) AF: 0.298 AC: 12301 AN: 41322

American (AMR) AF: 0.156 AC: 2384 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3464

East Asian (EAS) AF: 0.136 AC: 695 AN: 5110

South Asian (SAS) AF: 0.215 AC: 1035 AN: 4808

European-Finnish (FIN) AF: 0.173 AC: 1823 AN: 10512

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12288 AN: 67976

Other (OTH) AF: 0.218 AC: 458 AN: 2102

Alfa AF: 0.195 Hom.: 9321

Bravo AF: 0.213

Asia WGS AF: 0.177 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
DANN	Benign	0.67
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6092179; hg19: chr20-54379033;