chr1-58928786-C-A

Position:

• chr1-58928786-C-A

Variant summary

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

The ENST00000665413.1(LINC02777):​n.54+3058G>T 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 0.486 in 151,632 control chromosomes in the GnomAD database, including 18,219 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 0.49 (18219 hom., cov: 31)
• Consequence: LINC02777 ENST00000665413.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

LINC02777 (HGNC:54297): (long intergenic non-protein coding RNA 2777)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02777	ENST00000665413.1	n.54+3058G>T		intron_variant, non_coding_transcript_variant
LINC02777	ENST00000669325.1	n.112+1269G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73655 AN: 151514 Hom.: 18209 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.486 AC: 73699 AN: 151632 Hom.: 18219 Cov.: 31 AF XY: 0.491 AC XY: 36345 AN XY: 74058

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.475

Alfa AF: 0.425 Hom.: 2524

Bravo AF: 0.497

Asia WGS AF: 0.569 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2764915; hg19: chr1-59394458;