rs7665842

Variant names:

• chr4-141572742-C-T
• rs7665842
• ENST00000508388.1:n.87-2760G>A

Variant summary

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

The ENST00000508388.1(LINC02276):​n.87-2760G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,012 control chromosomes in the GnomAD database, including 45,039 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 0.77 (45039 hom., cov: 31)
• Consequence: LINC02276 ENST00000508388.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 4 publications found

Genes affected

LINC02276 (HGNC:53192): (long intergenic non-protein coding RNA 2276)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508388.1. 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
	LINC02276	ENST00000508388.1	TSL:3	n.87-2760G>A		intron	N/A
	LINC02276	ENST00000743752.1		n.293-2760G>A		intron	N/A
	LINC02276	ENST00000743753.1		n.284+3250G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116616 AN: 151894 Hom.: 44991 Cov.: 31

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.768 AC: 116722 AN: 152012 Hom.: 45039 Cov.: 31 AF XY: 0.771 AC XY: 57248 AN XY: 74276

African (AFR) AF: 0.796 AC: 33019 AN: 41492

American (AMR) AF: 0.778 AC: 11864 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2591 AN: 3468

East Asian (EAS) AF: 0.992 AC: 5125 AN: 5164

South Asian (SAS) AF: 0.816 AC: 3933 AN: 4820

European-Finnish (FIN) AF: 0.742 AC: 7826 AN: 10550

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49921 AN: 67966

Other (OTH) AF: 0.736 AC: 1553 AN: 2110

Alfa AF: 0.760 Hom.: 5466

Bravo AF: 0.773

Asia WGS AF: 0.883 AC: 3065 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.46
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7665842; hg19: chr4-142493895;