1-244031540-C-T

Position:

• chr1-244031540-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+4106C>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 0.607 in 152,090 control chromosomes in the GnomAD database, including 30,126 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 0.61 (30126 hom., cov: 33)
• Consequence: LINC02774 NR_033883.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02774	NR_033883.1	n.1053+4106C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02774	ENST00000440494.1	n.1053+4106C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92249 AN: 151972 Hom.: 30071 Cov.: 33

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.607 AC: 92365 AN: 152090 Hom.: 30126 Cov.: 33 AF XY: 0.607 AC XY: 45124 AN XY: 74340

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.624

Alfa AF: 0.519 Hom.: 17441

Bravo AF: 0.627

Asia WGS AF: 0.636 AC: 2204 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2454221; hg19: chr1-244194842;