ENST00000426413.2:n.106-22904C>T

Variant names:

• chr7-119823778-G-A
• rs10085666
• ENST00000426413.2:n.106-22904C>T

Variant summary

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

The ENST00000426413.2(LINC02476):​n.106-22904C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,058 control chromosomes in the GnomAD database, including 54,437 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 0.81 (54437 hom., cov: 31)
• Consequence: LINC02476 ENST00000426413.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 0 publications found

Genes affected

LINC02476 (HGNC:53419): (long intergenic non-protein coding RNA 2476)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02476	NR_131960.1	n.84-7198C>T		intron_variant	Intron 1 of 4
LINC02476	NR_131961.1	n.84-22904C>T		intron_variant	Intron 1 of 3
LINC02476	NR_131962.1	n.84-22904C>T		intron_variant	Intron 1 of 2
LINC02476	NR_131963.1	n.84-22904C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02476	ENST00000426413.2	n.106-22904C>T		intron_variant	Intron 1 of 3	2
LINC02476	ENST00000431071.5	n.84-22904C>T		intron_variant	Intron 1 of 2	4
LINC02476	ENST00000660268.1	n.84-22904C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122657 AN: 151940 Hom.: 54433 Cov.: 31

Gnomad AFR AF: 0.399

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.807 AC: 122682 AN: 152058 Hom.: 54437 Cov.: 31 AF XY: 0.815 AC XY: 60594 AN XY: 74334

African (AFR) AF: 0.398 AC: 16476 AN: 41360

American (AMR) AF: 0.908 AC: 13874 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3338 AN: 3468

East Asian (EAS) AF: 0.996 AC: 5147 AN: 5170

South Asian (SAS) AF: 0.964 AC: 4654 AN: 4826

European-Finnish (FIN) AF: 0.992 AC: 10528 AN: 10614

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65716 AN: 68018

Other (OTH) AF: 0.841 AC: 1777 AN: 2112

Alfa AF: 0.912 Hom.: 74499

Bravo AF: 0.780

Asia WGS AF: 0.927 AC: 3221 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.31
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10085666; hg19: chr7-119463832;