ENST00000813368.1:n.410-20745C>T

Variant names:

• chr9-6697128-C-T
• rs10739110
• ENST00000813368.1:n.410-20745C>T

Variant summary

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

The ENST00000813368.1(LINC02851):​n.410-20745C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,962 control chromosomes in the GnomAD database, including 10,787 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 0.37 (10787 hom., cov: 32)
• Consequence: LINC02851 ENST00000813368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 2 publications found

Genes affected

LINC02851 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 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
LINC02851	ENST00000813368.1	n.410-20745C>T		intron_variant	Intron 2 of 2
LINC02851	ENST00000813369.1	n.410-7325C>T		intron_variant	Intron 2 of 3
LINC02851	ENST00000813370.1	n.407-7325C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56600 AN: 151844 Hom.: 10773 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.373 AC: 56641 AN: 151962 Hom.: 10787 Cov.: 32 AF XY: 0.371 AC XY: 27550 AN XY: 74302

African (AFR) AF: 0.395 AC: 16341 AN: 41408

American (AMR) AF: 0.290 AC: 4421 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1468 AN: 3464

East Asian (EAS) AF: 0.473 AC: 2442 AN: 5160

South Asian (SAS) AF: 0.336 AC: 1617 AN: 4818

European-Finnish (FIN) AF: 0.403 AC: 4253 AN: 10566

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24883 AN: 67982

Other (OTH) AF: 0.370 AC: 778 AN: 2104

Alfa AF: 0.362 Hom.: 21176

Bravo AF: 0.369

Asia WGS AF: 0.387 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.8
DANN	Benign	0.84
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10739110; hg19: chr9-6697128;