rs646860

Variant names:

• chr1-60132629-G-A
• rs646860
• ENST00000456878.1:n.100-15884G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-60132629-G-A
• chr1-60132629-G-C

Variant summary

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

The ENST00000659925.1(LINC02778):​n.135-215G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,850 control chromosomes in the GnomAD database, including 35,231 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 0.68 (35231 hom., cov: 31)
• Consequence: LINC02778 ENST00000659925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 2 publications found

Genes affected

LINC02778 (HGNC:54298): (long intergenic non-protein coding RNA 2778)

ENSG00000303283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659925.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02778	ENST00000456878.1	TSL:5	n.100-15884G>A		intron	N/A
	LINC02778	ENST00000659925.1		n.135-215G>A		intron	N/A
	ENSG00000303283	ENST00000793364.1		n.369+101C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103127 AN: 151732 Hom.: 35204 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.680 AC: 103200 AN: 151850 Hom.: 35231 Cov.: 31 AF XY: 0.679 AC XY: 50351 AN XY: 74206

African (AFR) AF: 0.691 AC: 28609 AN: 41404

American (AMR) AF: 0.642 AC: 9808 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2211 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2733 AN: 5142

South Asian (SAS) AF: 0.779 AC: 3745 AN: 4808

European-Finnish (FIN) AF: 0.646 AC: 6801 AN: 10530

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47079 AN: 67910

Other (OTH) AF: 0.669 AC: 1414 AN: 2114

Alfa AF: 0.686 Hom.: 4433

Bravo AF: 0.672

Asia WGS AF: 0.659 AC: 2291 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.26
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs646860; hg19: chr1-60598301;