1-60141731-G-C

Variant names:

• chr1-60141731-G-C
• rs1462936
• ENST00000456878.1:n.100-6782G>C

Variant summary

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

The ENST00000659925.1(LINC02778):​n.472-6782G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0071 in 152,060 control chromosomes in the GnomAD database, including 19 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 0.0071 (19 hom., cov: 33)
• Consequence: LINC02778 ENST00000659925.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 0 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0533 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.100-6782G>C		intron	N/A
	LINC02778	ENST00000659925.1		n.472-6782G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00708 AC: 1075 AN: 151942 Hom.: 19 Cov.: 33

Gnomad AFR AF: 0.00157

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0148

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.0590

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.00377

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00440

Gnomad OTH AF: 0.00911

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

GnomAD4 genome AF: 0.00710 AC: 1079 AN: 152060 Hom.: 19 Cov.: 33 AF XY: 0.00797 AC XY: 593 AN XY: 74358

African (AFR) AF: 0.00157 AC: 65 AN: 41514

American (AMR) AF: 0.0151 AC: 230 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3468

East Asian (EAS) AF: 0.0587 AC: 303 AN: 5158

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4824

European-Finnish (FIN) AF: 0.00377 AC: 40 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00440 AC: 299 AN: 67922

Other (OTH) AF: 0.00949 AC: 20 AN: 2108

Alfa AF: 0.00475 Hom.: 0

Bravo AF: 0.00807

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	15
DANN	Benign	0.66
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1462936;

hg19: chr1-60607403;