13-78581477-C-T

Variant names:

• chr13-78581477-C-T
• rs1409005
• ENST00000607862.5:n.3316C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000607862.5(OBI1-AS1):​n.3316C>T 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 0.125 in 152,030 control chromosomes in the GnomAD database, including 1,430 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 (1430 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: OBI1-AS1 ENST00000607862.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.54
• Publications: 3 publications found

Genes affected

OBI1-AS1 (HGNC:42700): (OBI1 antisense RNA 1)

ENSG00000296474 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OBI1-AS1	NR_047001.1	n.385-23824C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OBI1-AS1	ENST00000607862.5	n.3316C>T		non_coding_transcript_exon_variant	Exon 3 of 3	1
OBI1-AS1	ENST00000739945.1	n.1479C>T		non_coding_transcript_exon_variant	Exon 2 of 2
OBI1-AS1	ENST00000430549.6	n.429+2814C>T		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18912 AN: 151912 Hom.: 1418 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.115

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

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.125 AC: 18951 AN: 152030 Hom.: 1430 Cov.: 32 AF XY: 0.124 AC XY: 9231 AN XY: 74338

African (AFR) AF: 0.203 AC: 8407 AN: 41418

American (AMR) AF: 0.0896 AC: 1369 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0818 AC: 284 AN: 3470

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5176

South Asian (SAS) AF: 0.148 AC: 715 AN: 4820

European-Finnish (FIN) AF: 0.0892 AC: 944 AN: 10578

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.0993 AC: 6750 AN: 67968

Other (OTH) AF: 0.114 AC: 241 AN: 2114

Alfa AF: 0.0934 Hom.: 335

Bravo AF: 0.128

Asia WGS AF: 0.0880 AC: 308 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	15
DANN	Benign	0.71
PhyloP100		3.5
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1409005; hg19: chr13-79155612;