2-114027820-T-G

Variant names:

• chr2-114027820-T-G
• rs400960
• ENST00000828060.1:n.409-21T>G

Variant summary

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

The ENST00000828060.1(LINC01191):​n.409-21T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,092 control chromosomes in the GnomAD database, including 35,545 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 0.68 (35545 hom., cov: 33)
• Consequence: LINC01191 ENST00000828060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 4 publications found

Genes affected

LINC01191 (HGNC:49595): (long intergenic non-protein coding RNA 1191)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01191	NR_148509.1	n.561-21T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01191	ENST00000828060.1	n.409-21T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103525 AN: 151974 Hom.: 35512 Cov.: 33

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.681 AC: 103607 AN: 152092 Hom.: 35545 Cov.: 33 AF XY: 0.676 AC XY: 50241 AN XY: 74350

African (AFR) AF: 0.756 AC: 31402 AN: 41514

American (AMR) AF: 0.579 AC: 8850 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2359 AN: 3472

East Asian (EAS) AF: 0.578 AC: 2984 AN: 5160

South Asian (SAS) AF: 0.586 AC: 2821 AN: 4816

European-Finnish (FIN) AF: 0.663 AC: 7010 AN: 10570

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.676 AC: 45960 AN: 67966

Other (OTH) AF: 0.682 AC: 1441 AN: 2112

Alfa AF: 0.662 Hom.: 7775

Bravo AF: 0.681

Asia WGS AF: 0.578 AC: 2010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.60
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs400960; hg19: chr2-114785397;