13-77990531-A-G

Variant names:

• chr13-77990531-A-G
• rs4884082
• ENST00000607862.5:n.230+70613A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662401.1(LINC01069):​n.182T>C 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 0.204 in 152,046 control chromosomes in the GnomAD database, including 3,711 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 0.20 (3711 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01069 ENST00000662401.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 2 publications found

Genes affected

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

LINC01069 (HGNC:49109): (long intergenic non-protein coding RNA 1069)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662401.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01069	NR_108076.1		n.160-923T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBI1-AS1	ENST00000607862.5	TSL:1	n.230+70613A>G		intron	N/A
	LINC01069	ENST00000452933.2	TSL:5	n.145T>C		non_coding_transcript_exon	Exon 2 of 5
	LINC01069	ENST00000662401.1		n.182T>C		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31004 AN: 151928 Hom.: 3703 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.197

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: 0.204 AC: 31044 AN: 152046 Hom.: 3711 Cov.: 32 AF XY: 0.209 AC XY: 15505 AN XY: 74308

African (AFR) AF: 0.250 AC: 10368 AN: 41490

American (AMR) AF: 0.255 AC: 3890 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 451 AN: 3470

East Asian (EAS) AF: 0.541 AC: 2791 AN: 5160

South Asian (SAS) AF: 0.253 AC: 1221 AN: 4818

European-Finnish (FIN) AF: 0.172 AC: 1821 AN: 10600

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9986 AN: 67936

Other (OTH) AF: 0.195 AC: 413 AN: 2114

Alfa AF: 0.169 Hom.: 313

Bravo AF: 0.215

Asia WGS AF: 0.329 AC: 1140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.62
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4884082; hg19: chr13-78564666;