2-188189384-T-C

Position:

• chr2-188189384-T-C

Variant summary

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

The NR_126396.1(LINC01090):​n.226-23476A>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 0.923 in 152,142 control chromosomes in the GnomAD database, including 65,574 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 0.92 (65574 hom., cov: 31)
• Consequence: LINC01090 NR_126396.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01090	NR_126396.1	n.226-23476A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01090	ENST00000434418.2	n.226-23476A>G		intron_variant, non_coding_transcript_variant		5
LINC01090	ENST00000632331.1	n.81-256A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140378 AN: 152024 Hom.: 65533 Cov.: 31

Gnomad AFR AF: 0.768

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.997

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.923 AC: 140477 AN: 152142 Hom.: 65574 Cov.: 31 AF XY: 0.926 AC XY: 68922 AN XY: 74400

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.962

Gnomad4 ASJ AF: 0.996

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.997

Gnomad4 FIN AF: 0.984

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.939

Alfa AF: 0.969 Hom.: 35441

Bravo AF: 0.914

Asia WGS AF: 0.991 AC: 3444 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4527172; hg19: chr2-189054111;