2-66728771-C-T

Variant names:

• chr2-66728771-C-T
• rs11126095
• ENST00000412944.1:n.310-1168C>T

Variant summary

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

The ENST00000412944.1(LINC01798):​n.310-1168C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,978 control chromosomes in the GnomAD database, including 8,708 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 0.32 (8708 hom., cov: 32)
• Consequence: LINC01798 ENST00000412944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 4 publications found

Genes affected

LINC01798 (HGNC:52588): (long intergenic non-protein coding RNA 1798)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 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
LINC01798	ENST00000412944.1	n.310-1168C>T		intron_variant	Intron 4 of 4	4
LINC01798	ENST00000653254.1	n.253-1168C>T		intron_variant	Intron 3 of 3
LINC01798	ENST00000715601.1	n.184+37048C>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49321 AN: 151860 Hom.: 8705 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.325 AC: 49357 AN: 151978 Hom.: 8708 Cov.: 32 AF XY: 0.325 AC XY: 24117 AN XY: 74274

African (AFR) AF: 0.187 AC: 7767 AN: 41486

American (AMR) AF: 0.406 AC: 6206 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1422 AN: 3472

East Asian (EAS) AF: 0.397 AC: 2037 AN: 5136

South Asian (SAS) AF: 0.387 AC: 1864 AN: 4812

European-Finnish (FIN) AF: 0.343 AC: 3614 AN: 10550

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25114 AN: 67948

Other (OTH) AF: 0.380 AC: 802 AN: 2108

Alfa AF: 0.359 Hom.: 10510

Bravo AF: 0.327

Asia WGS AF: 0.406 AC: 1411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.093
DANN	Benign	0.61
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs11126095; hg19: chr2-66955903;