rs12127679

Positions:

• chr1-244004499-C-T

Variant summary

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

The NR_033883.1(LINC02774):​n.354-559C>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 0.202 in 152,106 control chromosomes in the GnomAD database, including 3,401 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 0.20 (3401 hom., cov: 32)
• Consequence: LINC02774 NR_033883.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

Genes affected

LINC02774 (HGNC:27923): (long intergenic non-protein coding RNA 2774)

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 (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02774	NR_033883.1	n.354-559C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02774	ENST00000440494.1	n.354-559C>T		intron_variant, non_coding_transcript_variant		1
LINC02774	ENST00000652928.1	n.187-5522C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30651 AN: 151988 Hom.: 3382 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.202 AC: 30702 AN: 152106 Hom.: 3401 Cov.: 32 AF XY: 0.206 AC XY: 15336 AN XY: 74346

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.202

Alfa AF: 0.177 Hom.: 355

Bravo AF: 0.208

Asia WGS AF: 0.318 AC: 1106 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	0.81
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12127679; hg19: chr1-244167801;