rs10927101

Positions:

• chr1-244010570-C-A
• chr1-244010570-C-G
• chr1-244010570-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.527-127C>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 0.439 in 152,050 control chromosomes in the GnomAD database, including 15,216 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 0.44 (15213 hom., cov: 33)
  • Exomes 𝑓: 0.60 (3 hom.)
• Consequence: LINC02774 NR_033883.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02774	NR_033883.1	n.527-127C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02774	ENST00000440494.1	n.527-127C>A		intron_variant, non_coding_transcript_variant		1
LINC02774	ENST00000652928.1	n.259-127C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66691 AN: 151922 Hom.: 15197 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.448

GnomAD4 exome AF: 0.600 AC: 6 AN: 10 Hom.: 3 AF XY: 0.600 AC XY: 6 AN XY: 10

Gnomad4 ASJ exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.439 AC: 66754 AN: 152040 Hom.: 15213 Cov.: 33 AF XY: 0.441 AC XY: 32748 AN XY: 74308

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.450

Alfa AF: 0.389 Hom.: 18634

Bravo AF: 0.450

Asia WGS AF: 0.557 AC: 1935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10927101; hg19: chr1-244173872;