1-225449904-A-G

Variant names:

• chr1-225449904-A-G
• rs6426075
• ENST00000428642.1:n.122-2386T>C

Variant summary

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

The ENST00000433058.1(LINC02765):​n.62-1319T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,066 control chromosomes in the GnomAD database, including 53,069 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 0.83 (53069 hom., cov: 31)
• Consequence: LINC02765 ENST00000433058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 8 publications found

Genes affected

LINC02765 (HGNC:54285): (long intergenic non-protein coding RNA 2765)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433058.1. 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
	LINC02765	NR_187302.1		n.828-1319T>C		intron	N/A
	LINC02765	NR_187303.1		n.728-1319T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02765	ENST00000428642.1	TSL:3	n.122-2386T>C		intron	N/A
	LINC02765	ENST00000433058.1	TSL:2	n.62-1319T>C		intron	N/A
	LINC02765	ENST00000651771.1		n.425+575T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126463 AN: 151948 Hom.: 53035 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.832 AC: 126548 AN: 152066 Hom.: 53069 Cov.: 31 AF XY: 0.830 AC XY: 61681 AN XY: 74334

African (AFR) AF: 0.736 AC: 30509 AN: 41462

American (AMR) AF: 0.889 AC: 13579 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3226 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4247 AN: 5138

South Asian (SAS) AF: 0.669 AC: 3224 AN: 4816

European-Finnish (FIN) AF: 0.886 AC: 9397 AN: 10602

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59509 AN: 67994

Other (OTH) AF: 0.851 AC: 1790 AN: 2104

Alfa AF: 0.858 Hom.: 151420

Bravo AF: 0.833

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.41
PhyloP100		-0.66

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: rs6426075;

hg19: chr1-225637606;