rs17403780

chr1-191970658-T-A

Variant summary

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

The ENST00000430776.2(LINC02770):n.394+5245T>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 0.0508 in 152,266 control chromosomes in the GnomAD database, including 272 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 0.051 (272 hom., cov: 32)
• Consequence: LINC02770 ENST00000430776.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

Genes affected

LINC02770 (HGNC:54290): (long intergenic non-protein coding RNA 2770)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02770	ENST00000430776.2	n.394+5245T>A		intron_variant, non_coding_transcript_variant		1
LINC02770	ENST00000664489.1	n.353+5245T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7747 AN: 152148 Hom.: 272 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0194

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0813

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0508 AC: 7742 AN: 152266 Hom.: 272 Cov.: 32 AF XY: 0.0484 AC XY: 3605 AN XY: 74452

Gnomad4 AFR AF: 0.0147

Gnomad4 AMR AF: 0.0475

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.0432

Gnomad4 NFE AF: 0.0813

Gnomad4 OTH AF: 0.0469

Alfa AF: 0.0581 Hom.: 31

Bravo AF: 0.0501

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.0
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17403780; hg19: chr1-191939788;