1-212472676-C-T

Position:

• chr1-212472676-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_Moderate BA1

The NR_183725.1(LINC02771):​n.202+1G>A variant causes a splice donor, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,112 control chromosomes in the GnomAD database, including 21,523 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 (21523 hom., cov: 32)
• Consequence: LINC02771 NR_183725.1 splice_donor, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734

Genes affected

LINC02771 (HGNC:54291): (long intergenic non-protein coding RNA 2771)

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02771	NR_183725.1	n.202+1G>A		splice_donor_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02771	ENST00000661486.1	n.229+1G>A		splice_donor_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75018 AN: 151994 Hom.: 21487 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.494 AC: 75106 AN: 152112 Hom.: 21523 Cov.: 32 AF XY: 0.482 AC XY: 35880 AN XY: 74382

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.477

Alfa AF: 0.440 Hom.: 2098

Bravo AF: 0.517

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6694514; hg19: chr1-212646018;