ENST00000839501.1:n.98+7318A>G

Variant names:

• chr11-30727543-T-C
• rs963837
• ENST00000839501.1:n.98+7318A>G

Variant summary

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

The ENST00000839501.1(ENSG00000309197):​n.98+7318A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,078 control chromosomes in the GnomAD database, including 11,194 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 0.35 (11194 hom., cov: 33)
• Consequence: ENSG00000309197 ENST00000839501.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 42 publications found

Genes affected

ENSG00000309197 (HGNC:):

LINC02859 (HGNC:54399): (long intergenic non-protein coding RNA 2859)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02859	NR_187236.1	n.68+7318A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309197	ENST00000839501.1	n.98+7318A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53762 AN: 151960 Hom.: 11195 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.354 AC: 53763 AN: 152078 Hom.: 11194 Cov.: 33 AF XY: 0.355 AC XY: 26351 AN XY: 74316

African (AFR) AF: 0.125 AC: 5214 AN: 41546

American (AMR) AF: 0.432 AC: 6591 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1581 AN: 3466

East Asian (EAS) AF: 0.378 AC: 1949 AN: 5162

South Asian (SAS) AF: 0.273 AC: 1316 AN: 4814

European-Finnish (FIN) AF: 0.487 AC: 5138 AN: 10556

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30778 AN: 67962

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.410 Hom.: 30160

Bravo AF: 0.342

Asia WGS AF: 0.322 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.5
DANN	Benign	0.83
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs963837; hg19: chr11-30749090;