rs11728679

Variant names:

• chr4-188166932-C-T
• rs11728679
• ENST00000759581.1:n.217+6830C>T

Variant summary

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

The ENST00000759581.1(LINC02434):​n.217+6830C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,974 control chromosomes in the GnomAD database, including 1,460 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 0.14 (1460 hom., cov: 31)
• Consequence: LINC02434 ENST00000759581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 1 publications found

Genes affected

LINC02434 (HGNC:53365): (long intergenic non-protein coding RNA 2434)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02434	ENST00000759581.1	n.217+6830C>T		intron_variant	Intron 1 of 1
LINC02434	ENST00000759582.1	n.134+6813C>T		intron_variant	Intron 1 of 1
LINC02434	ENST00000759583.1	n.171+6813C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20652 AN: 151858 Hom.: 1461 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0739

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.136 AC: 20651 AN: 151974 Hom.: 1460 Cov.: 31 AF XY: 0.132 AC XY: 9828 AN XY: 74260

African (AFR) AF: 0.143 AC: 5943 AN: 41438

American (AMR) AF: 0.121 AC: 1843 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3470

East Asian (EAS) AF: 0.0743 AC: 382 AN: 5144

South Asian (SAS) AF: 0.0770 AC: 370 AN: 4806

European-Finnish (FIN) AF: 0.130 AC: 1377 AN: 10572

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9809 AN: 67966

Other (OTH) AF: 0.146 AC: 307 AN: 2108

Alfa AF: 0.137 Hom.: 163

Bravo AF: 0.136

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.66
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs11728679; hg19: chr4-189088086;