2-188189384-T-C

Variant names:

• chr2-188189384-T-C
• rs4527172
• ENST00000434418.2:n.226-23476A>G

Variant summary

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

The NR_126396.1(LINC01090):​n.226-23476A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_126396.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01090	NR_126396.1		n.226-23476A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01090	ENST00000434418.2	TSL:5	n.226-23476A>G		intron	N/A
	LINC01090	ENST00000632331.1	TSL:5	n.81-256A>G		intron	N/A
	LINC01090	ENST00000757430.1		n.230-256A>G		intron	N/A

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

African (AFR) AF: 0.768 AC: 31881 AN: 41496

American (AMR) AF: 0.962 AC: 14673 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3457 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5175 AN: 5176

South Asian (SAS) AF: 0.997 AC: 4807 AN: 4822

European-Finnish (FIN) AF: 0.984 AC: 10447 AN: 10622

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66855 AN: 67992

Other (OTH) AF: 0.939 AC: 1981 AN: 2110

Alfa AF: 0.968 Hom.: 39344

Bravo AF: 0.914

Asia WGS AF: 0.991 AC: 3444 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.66
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs4527172; hg19: chr2-189054111;