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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02276	XR_939260.3	n.253-2760G>A		intron_variant	Intron 2 of 3
LINC02276	XR_939261.3	n.252+3250G>A		intron_variant	Intron 2 of 2
LINC02276	XR_939262.3	n.255-2760G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02276	ENST00000508388.1	n.87-2760G>A		intron_variant	Intron 1 of 1	3
LINC02276	ENST00000743752.1	n.293-2760G>A		intron_variant	Intron 2 of 3
LINC02276	ENST00000743753.1	n.284+3250G>A		intron_variant	Intron 2 of 2

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 v4.3

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;