chr1-58903275-G-T

Variant names:

• chr1-58903275-G-T
• rs927743
• ENST00000634763.1:n.180+293C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634763.1(LINC02777):​n.180+293C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,928 control chromosomes in the GnomAD database, including 17,038 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 0.47 (17038 hom., cov: 32)
• Consequence: LINC02777 ENST00000634763.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 4 publications found

Genes affected

LINC02777 (HGNC:54297): (long intergenic non-protein coding RNA 2777)

JUN-DT (HGNC:49450): (JUN divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02777	NR_183655.1	n.571+293C>A		intron_variant	Intron 1 of 3
LINC02777	NR_183656.1	n.571+293C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02777	ENST00000634763.1	n.180+293C>A		intron_variant	Intron 1 of 3	2
LINC02777	ENST00000635492.1	n.112+293C>A		intron_variant	Intron 1 of 4	5
LINC02777	ENST00000653076.1	n.165+293C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71180 AN: 151810 Hom.: 17018 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.469 AC: 71236 AN: 151928 Hom.: 17038 Cov.: 32 AF XY: 0.475 AC XY: 35258 AN XY: 74266

African (AFR) AF: 0.505 AC: 20895 AN: 41414

American (AMR) AF: 0.577 AC: 8816 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3464

East Asian (EAS) AF: 0.495 AC: 2551 AN: 5158

South Asian (SAS) AF: 0.626 AC: 3011 AN: 4810

European-Finnish (FIN) AF: 0.439 AC: 4640 AN: 10558

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28490 AN: 67934

Other (OTH) AF: 0.469 AC: 991 AN: 2112

Alfa AF: 0.435 Hom.: 45523

Bravo AF: 0.480

Asia WGS AF: 0.577 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.55
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs927743; hg19: chr1-59368947;