rs525566

Positions:

• chr1-109833073-G-A

Variant summary

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

The XR_001738180.3(LINC01768):​n.600G>A 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 0.68 in 152,066 control chromosomes in the GnomAD database, including 35,650 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 0.68 (35650 hom., cov: 31)
• Consequence: LINC01768 XR_001738180.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

LINC01768 (HGNC:52558): (long intergenic non-protein coding RNA 1768)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01768	XR_001738180.3	n.600G>A		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01768	ENST00000453347.1	n.292-227G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103395 AN: 151948 Hom.: 35618 Cov.: 31

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.680 AC: 103470 AN: 152066 Hom.: 35650 Cov.: 31 AF XY: 0.676 AC XY: 50244 AN XY: 74332

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.691

Alfa AF: 0.679 Hom.: 69876

Bravo AF: 0.678

Asia WGS AF: 0.627 AC: 2183 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	0.24
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs525566; hg19: chr1-110375695;