rs2764915

Variant names:

• chr1-58928786-C-A
• rs2764915
• ENST00000665413.1:n.54+3058G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-58928786-C-A
• chr1-58928786-C-G
• chr1-58928786-C-T

Variant summary

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

The ENST00000665413.1(LINC02777):​n.54+3058G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,632 control chromosomes in the GnomAD database, including 18,219 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 0.49 (18219 hom., cov: 31)
• Consequence: LINC02777 ENST00000665413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02777	ENST00000665413.1	n.54+3058G>T		intron_variant	Intron 1 of 3
LINC02777	ENST00000669325.1	n.112+1269G>T		intron_variant	Intron 1 of 4
JUN-DT	ENST00000715609.1	n.103-10828C>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73655 AN: 151514 Hom.: 18209 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.486 AC: 73699 AN: 151632 Hom.: 18219 Cov.: 31 AF XY: 0.491 AC XY: 36345 AN XY: 74058

African (AFR) AF: 0.507 AC: 20951 AN: 41314

American (AMR) AF: 0.587 AC: 8949 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1446 AN: 3464

East Asian (EAS) AF: 0.483 AC: 2482 AN: 5144

South Asian (SAS) AF: 0.641 AC: 3065 AN: 4778

European-Finnish (FIN) AF: 0.462 AC: 4856 AN: 10520

Middle Eastern (MID) AF: 0.445 AC: 129 AN: 290

European-Non Finnish (NFE) AF: 0.449 AC: 30457 AN: 67858

Other (OTH) AF: 0.475 AC: 1002 AN: 2110

Alfa AF: 0.429 Hom.: 2638

Bravo AF: 0.497

Asia WGS AF: 0.569 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.50
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs2764915; hg19: chr1-59394458;