20-44225494-A-G

Variant names:

• chr20-44225494-A-G
• rs6017291
• ENST00000439943.5:n.908A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439943.5(OSER1-DT):​n.908A>G 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 0.123 in 151,460 control chromosomes in the GnomAD database, including 1,585 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 0.12 (1585 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OSER1-DT ENST00000439943.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649

Genes affected

OSER1-DT (HGNC:48585): (OSER1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSER1-DT	NR_038337.2	n.1196A>G		non_coding_transcript_exon_variant	Exon 3 of 3
OSER1-DT	NR_038338.2	n.1065A>G		non_coding_transcript_exon_variant	Exon 3 of 3
OSER1-DT	NR_038339.2	n.908A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSER1-DT	ENST00000439943.5	n.908A>G		non_coding_transcript_exon_variant	Exon 3 of 3	1
OSER1-DT	ENST00000442383.1	n.949A>G		non_coding_transcript_exon_variant	Exon 2 of 2	1
OSER1-DT	ENST00000435163.5	n.1426A>G		non_coding_transcript_exon_variant	Exon 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18592 AN: 151342 Hom.: 1576 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.115

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.123 AC: 18625 AN: 151460 Hom.: 1585 Cov.: 32 AF XY: 0.128 AC XY: 9459 AN XY: 73950

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.0806

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0506

Gnomad4 NFE AF: 0.0669

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0841 Hom.: 1124

Bravo AF: 0.135

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6017291; hg19: chr20-42854134;