2-114027820-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_148509.1(LINC01191):n.561-21T>G variant causes a intron, non coding transcript 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 NR_148509.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

LINC01191 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01191	NR_148509.1	n.561-21T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.682

Alfa AF: 0.616 Hom.: 1817

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs400960; hg19: chr2-114785397;