rs1795030

chr1-214124300-A-Gchr1-214124300-A-T

Variant summary

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

The ENST00000637598.1(LINC02775):n.662-51862T>C 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 0.527 in 152,038 control chromosomes in the GnomAD database, including 22,684 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 0.53 (22684 hom., cov: 31)
• Consequence: LINC02775 ENST00000637598.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

Genes affected

LINC02775 (HGNC:54294): (long intergenic non-protein coding RNA 2775)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02775	ENST00000637598.1	n.662-51862T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79963 AN: 151918 Hom.: 22649 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.527 AC: 80051 AN: 152038 Hom.: 22684 Cov.: 31 AF XY: 0.539 AC XY: 40062 AN XY: 74316

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.497

Alfa AF: 0.433 Hom.: 14288

Bravo AF: 0.535

Asia WGS AF: 0.840 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.82
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1795030; hg19: chr1-214297643;