rs273370

chr5-5035083-G-A

Variant summary

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

The NR_026994.1(LINC01020):n.179+546G>A 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 0.804 in 151,984 control chromosomes in the GnomAD database, including 51,090 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 0.80 (51090 hom., cov: 31)
• Consequence: LINC01020 NR_026994.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

LINC01020 (HGNC:27968): (long intergenic non-protein coding RNA 1020)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01020	NR_026994.1	n.179+546G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01020	ENST00000659550.1	n.205-31820G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122241 AN: 151866 Hom.: 51092 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.804 AC: 122270 AN: 151984 Hom.: 51090 Cov.: 31 AF XY: 0.808 AC XY: 60004 AN XY: 74302

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.819

Alfa AF: 0.848 Hom.: 6980

Bravo AF: 0.792

Asia WGS AF: 0.819 AC: 2841 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.29
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs273370; hg19: chr5-5035196;