rs6092179

Positions:

• chr20-55803977-C-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105372677 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372677	XR_936887.2	n.78C>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.218

Alfa AF: 0.190 Hom.: 5388

Bravo AF: 0.213

Asia WGS AF: 0.177 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6092179; hg19: chr20-54379033;