7-119932337-C-T

Variant names:

• chr7-119932337-C-T
• rs10231641
• ENST00000804424.1:n.631+11684G>A

Variant summary

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

The ENST00000804424.1(LINC02476):​n.631+11684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 151,886 control chromosomes in the GnomAD database, including 53,530 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 0.84 (53530 hom., cov: 30)
• Consequence: LINC02476 ENST00000804424.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804424.1. 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
	LINC02476	ENST00000804424.1		n.631+11684G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126708 AN: 151768 Hom.: 53466 Cov.: 30

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.835 AC: 126834 AN: 151886 Hom.: 53530 Cov.: 30 AF XY: 0.834 AC XY: 61863 AN XY: 74204

African (AFR) AF: 0.952 AC: 39471 AN: 41460

American (AMR) AF: 0.825 AC: 12572 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2644 AN: 3466

East Asian (EAS) AF: 0.998 AC: 5165 AN: 5176

South Asian (SAS) AF: 0.817 AC: 3930 AN: 4812

European-Finnish (FIN) AF: 0.757 AC: 7967 AN: 10518

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52469 AN: 67894

Other (OTH) AF: 0.832 AC: 1758 AN: 2112

Alfa AF: 0.791 Hom.: 63716

Bravo AF: 0.845

Asia WGS AF: 0.926 AC: 3210 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.50
PhyloP100		0.16

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: rs10231641;

hg19: chr7-119572391;