chr2-188280414-A-T

Variant names:

• chr2-188280414-A-T
• rs6718697
• ENST00000415357.1:n.168+7053T>A

Variant summary

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

The ENST00000415357.1(LINC01090):​n.168+7053T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,108 control chromosomes in the GnomAD database, including 3,621 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 0.20 (3621 hom., cov: 33)
• Consequence: LINC01090 ENST00000415357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01090	NR_126396.1	n.225+7053T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01090	ENST00000415357.1	n.168+7053T>A		intron_variant	Intron 1 of 1	3
LINC01090	ENST00000434418.2	n.225+7053T>A		intron_variant	Intron 1 of 3	5
LINC01090	ENST00000632331.1	n.81-91286T>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30054 AN: 151990 Hom.: 3603 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.198 AC: 30135 AN: 152108 Hom.: 3621 Cov.: 33 AF XY: 0.194 AC XY: 14397 AN XY: 74356

African (AFR) AF: 0.335 AC: 13880 AN: 41492

American (AMR) AF: 0.152 AC: 2323 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3466

East Asian (EAS) AF: 0.0513 AC: 266 AN: 5182

South Asian (SAS) AF: 0.0719 AC: 347 AN: 4826

European-Finnish (FIN) AF: 0.162 AC: 1714 AN: 10596

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10631 AN: 67958

Other (OTH) AF: 0.188 AC: 395 AN: 2106

Alfa AF: 0.181 Hom.: 369

Bravo AF: 0.202

Asia WGS AF: 0.105 AC: 363 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.25
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs6718697; hg19: chr2-189145141;