rs2760101

Positions:

• chr13-79567776-A-G
• chr13-79567776-A-T

Variant summary

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

The NR_125772.1(LINC01068):​n.81+969A>G variant causes a intron, non coding transcript 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 NR_125772.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01068	NR_125772.1	n.81+969A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01068	ENST00000661483.1	n.130+969A>G		intron_variant, non_coding_transcript_variant
LINC01068	ENST00000450187.2	n.62+969A>G		intron_variant, non_coding_transcript_variant		5
LINC01068	ENST00000620874.2	n.123+969A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.564

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2760101; hg19: chr13-80141911;