20-44225494-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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. Variant has been reported in ClinVar as (no stars).

• 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
• Publications: 11 publications found

Genes affected

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

ENSG00000307782 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439943.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSER1-DT	NR_038337.2		n.1196A>G		non_coding_transcript_exon	Exon 3 of 3
	OSER1-DT	NR_038338.2		n.1065A>G		non_coding_transcript_exon	Exon 3 of 3
	OSER1-DT	NR_038339.2		n.908A>G		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSER1-DT	ENST00000439943.5	TSL:1	n.908A>G		non_coding_transcript_exon	Exon 3 of 3
	OSER1-DT	ENST00000442383.1	TSL:1	n.949A>G		non_coding_transcript_exon	Exon 2 of 2
	OSER1-DT	ENST00000435163.5	TSL:3	n.1426A>G		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 12

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.166 AC: 6866 AN: 41258

American (AMR) AF: 0.231 AC: 3520 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0806 AC: 279 AN: 3462

East Asian (EAS) AF: 0.322 AC: 1663 AN: 5164

South Asian (SAS) AF: 0.199 AC: 954 AN: 4788

European-Finnish (FIN) AF: 0.0506 AC: 526 AN: 10400

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0669 AC: 4538 AN: 67866

Other (OTH) AF: 0.116 AC: 244 AN: 2100

Alfa AF: 0.0914 Hom.: 1979

Bravo AF: 0.135

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.79
PhyloP100		0.65

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6017291;

hg19: chr20-42854134;