chr13-79567776-A-G

Variant names:

• chr13-79567776-A-G
• rs2760101
• ENST00000450187.2:n.62+969A>G

Variant summary

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

The ENST00000620874.3(LINC01068):​n.210+969A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,084 control chromosomes in the GnomAD database, including 27,532 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 0.59 (27532 hom., cov: 32)
• Consequence: LINC01068 ENST00000620874.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 3 publications found

Genes affected

LINC01068 (HGNC:49106): (long intergenic non-protein coding RNA 1068)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000620874.3. 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
	LINC01068	NR_125772.1		n.81+969A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01068	ENST00000450187.2	TSL:5	n.62+969A>G		intron	N/A
	LINC01068	ENST00000620874.3	TSL:3	n.210+969A>G		intron	N/A
	LINC01068	ENST00000661483.2		n.153+969A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90064 AN: 151966 Hom.: 27509 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.568

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.593 AC: 90131 AN: 152084 Hom.: 27532 Cov.: 32 AF XY: 0.582 AC XY: 43245 AN XY: 74342

African (AFR) AF: 0.716 AC: 29710 AN: 41504

American (AMR) AF: 0.456 AC: 6965 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2240 AN: 3466

East Asian (EAS) AF: 0.298 AC: 1542 AN: 5178

South Asian (SAS) AF: 0.557 AC: 2688 AN: 4822

European-Finnish (FIN) AF: 0.469 AC: 4961 AN: 10576

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.592 AC: 40245 AN: 67956

Other (OTH) AF: 0.564 AC: 1193 AN: 2116

Alfa AF: 0.454 Hom.: 1167

Bravo AF: 0.590

Asia WGS AF: 0.437 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.18
DANN	Benign	0.37
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2760101; hg19: chr13-80141911;