chr1-244033108-C-T

Position:

• chr1-244033108-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.1053+5674C>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 0.361 in 152,064 control chromosomes in the GnomAD database, including 10,712 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 0.36 (10712 hom., cov: 32)
• Consequence: LINC02774 NR_033883.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02774	NR_033883.1	n.1053+5674C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02774	ENST00000440494.1	n.1053+5674C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54882 AN: 151946 Hom.: 10692 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.361 AC: 54944 AN: 152064 Hom.: 10712 Cov.: 32 AF XY: 0.365 AC XY: 27116 AN XY: 74326

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.427

Alfa AF: 0.336 Hom.: 4109

Bravo AF: 0.370

Asia WGS AF: 0.529 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2047137; hg19: chr1-244196410;