rs1399685

Variant names:

• chr2-146870842-T-A
• rs1399685
• ENST00000450667.2:n.1295+3195T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000450667.2(LINC01911):​n.1295+3195T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0311 in 152,222 control chromosomes in the GnomAD database, including 106 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 0.031 (106 hom., cov: 32)
• Consequence: LINC01911 ENST00000450667.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 2 publications found

Genes affected

LINC01911 (HGNC:52730): (long intergenic non-protein coding RNA 1911)

ENSG00000302891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0311 (4736/152222) while in subpopulation NFE AF = 0.0498 (3389/68002). AF 95% confidence interval is 0.0484. There are 106 homozygotes in GnomAd4. There are 2206 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 106 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01911	NR_187164.1	n.1581+3195T>A		intron_variant	Intron 9 of 9
LINC01911	NR_187165.1	n.1532+3195T>A		intron_variant	Intron 9 of 9
LINC01911	NR_187166.1	n.1365+3195T>A		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01911	ENST00000450667.2	n.1295+3195T>A		intron_variant	Intron 10 of 10	5
LINC01911	ENST00000654856.1	n.1004+3195T>A		intron_variant	Intron 6 of 6
LINC01911	ENST00000655662.1	n.1045+3195T>A		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.0311 AC: 4738 AN: 152104 Hom.: 106 Cov.: 32

Gnomad AFR AF: 0.00896

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0306

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00787

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0311 AC: 4736 AN: 152222 Hom.: 106 Cov.: 32 AF XY: 0.0296 AC XY: 2206 AN XY: 74418

African (AFR) AF: 0.00893 AC: 371 AN: 41544

American (AMR) AF: 0.0305 AC: 466 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0158 AC: 55 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.00767 AC: 37 AN: 4824

European-Finnish (FIN) AF: 0.0291 AC: 309 AN: 10608

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0498 AC: 3389 AN: 68002

Other (OTH) AF: 0.0397 AC: 84 AN: 2116

Alfa AF: 0.0389 Hom.: 13

Bravo AF: 0.0313

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.7
DANN	Benign	0.77
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1399685; hg19: chr2-147628410;