rs11038830

Variant names:

• chr11-46240471-T-C
• rs11038830
• ENST00000812292.1:n.104+3183A>G

Variant summary

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

The ENST00000812292.1(LINC02710):​n.104+3183A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,212 control chromosomes in the GnomAD database, including 1,663 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 (1663 hom., cov: 32)
• Consequence: LINC02710 ENST00000812292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 5 publications found

Genes affected

LINC02710 (HGNC:54227): (long intergenic non-protein coding RNA 2710)

ENSG00000254639 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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
LINC02710	ENST00000812292.1	n.104+3183A>G		intron_variant	Intron 1 of 2
LINC02710	ENST00000812293.1	n.104+3183A>G		intron_variant	Intron 1 of 2
ENSG00000254639	ENST00000812432.1	n.343+1763T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21225 AN: 152094 Hom.: 1663 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.139 AC: 21232 AN: 152212 Hom.: 1663 Cov.: 32 AF XY: 0.137 AC XY: 10171 AN XY: 74446

African (AFR) AF: 0.203 AC: 8407 AN: 41506

American (AMR) AF: 0.0916 AC: 1402 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0982 AC: 341 AN: 3472

East Asian (EAS) AF: 0.112 AC: 584 AN: 5192

South Asian (SAS) AF: 0.106 AC: 511 AN: 4822

European-Finnish (FIN) AF: 0.0993 AC: 1053 AN: 10600

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8509 AN: 68006

Other (OTH) AF: 0.145 AC: 306 AN: 2110

Alfa AF: 0.130 Hom.: 3856

Bravo AF: 0.142

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.88
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs11038830; hg19: chr11-46262022;