chr4-129737474-C-T

Variant names:

• chr4-129737474-C-T
• rs6850594
• ENST00000500092.7:n.235+6834G>A

Variant summary

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

The ENST00000500092.7(LINC02466):​n.235+6834G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 151,962 control chromosomes in the GnomAD database, including 40,945 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 0.73 (40945 hom., cov: 32)
• Consequence: LINC02466 ENST00000500092.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 1 publications found

Genes affected

LINC02466 (HGNC:53405): (long intergenic non-protein coding RNA 2466)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02466	NR_110753.1	n.232+6834G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02466	ENST00000500092.7	n.235+6834G>A		intron_variant	Intron 3 of 4	1
LINC02466	ENST00000653323.1	n.187-10441G>A		intron_variant	Intron 2 of 3
LINC02466	ENST00000653915.1	n.97-10441G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111202 AN: 151844 Hom.: 40901 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.732 AC: 111299 AN: 151962 Hom.: 40945 Cov.: 32 AF XY: 0.727 AC XY: 54010 AN XY: 74280

African (AFR) AF: 0.770 AC: 31946 AN: 41478

American (AMR) AF: 0.682 AC: 10413 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2683 AN: 3468

East Asian (EAS) AF: 0.602 AC: 3100 AN: 5152

South Asian (SAS) AF: 0.660 AC: 3176 AN: 4814

European-Finnish (FIN) AF: 0.751 AC: 7936 AN: 10574

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49770 AN: 67898

Other (OTH) AF: 0.702 AC: 1482 AN: 2112

Alfa AF: 0.748 Hom.: 5320

Bravo AF: 0.728

Asia WGS AF: 0.648 AC: 2251 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.66
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs6850594; hg19: chr4-130658629;