chr8-91063415-A-C

Position:

• chr8-91063415-A-C

Variant summary

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

The ENST00000522817.3(OTUD6B-AS1):​n.838T>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 0.636 in 151,952 control chromosomes in the GnomAD database, including 31,193 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 0.64 (31192 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: OTUD6B-AS1 ENST00000522817.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

Genes affected

OTUD6B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OTUD6B-AS1	NR_110438.1	n.835T>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OTUD6B-AS1	ENST00000522817.3	n.838T>G		non_coding_transcript_exon_variant	3/3	2
OTUD6B-AS1	ENST00000657110.1	n.1872T>G		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96637 AN: 151830 Hom.: 31166 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.628

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.636 AC: 96703 AN: 151948 Hom.: 31192 Cov.: 32 AF XY: 0.632 AC XY: 46946 AN XY: 74276

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.630

Alfa AF: 0.649 Hom.: 14643

Bravo AF: 0.621

Asia WGS AF: 0.658 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4493873; hg19: chr8-92075643;