4-129737474-C-T

Position:

• chr4-129737474-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02466 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02466	NR_110753.1	n.232+6834G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02466	ENST00000500092.7	n.235+6834G>A		intron_variant		1
LINC02466	ENST00000653323.1	n.187-10441G>A		intron_variant
LINC02466	ENST00000653915.1	n.97-10441G>A		intron_variant

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

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.702

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6850594; hg19: chr4-130658629;