rs12090554

Variant names:

• chr1-185583216-G-A
• rs12090554
• ENST00000608417.6:n.167-19888C>T

Variant summary

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

The ENST00000608417.6(LINC01350):​n.167-19888C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,116 control chromosomes in the GnomAD database, including 2,179 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 0.15 (2179 hom., cov: 32)
• Consequence: LINC01350 ENST00000608417.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 4 publications found

Genes affected

LINC01350 (HGNC:50575): (long intergenic non-protein coding RNA 1350)

GS1-204I12.4 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01350	NR_110793.1	n.147-19888C>T		intron_variant	Intron 2 of 3
LOC107985239	XR_001738340.2	n.1067-96233G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01350	ENST00000608417.6	n.167-19888C>T		intron_variant	Intron 2 of 3	1
LINC01350	ENST00000439633.7	n.152-14321C>T		intron_variant	Intron 2 of 5	5
LINC01350	ENST00000609066.6	n.180-17520C>T		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23036 AN: 151998 Hom.: 2178 Cov.: 32

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.151 AC: 23032 AN: 152116 Hom.: 2179 Cov.: 32 AF XY: 0.154 AC XY: 11462 AN XY: 74346

African (AFR) AF: 0.0376 AC: 1562 AN: 41540

American (AMR) AF: 0.142 AC: 2167 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3468

East Asian (EAS) AF: 0.0828 AC: 428 AN: 5172

South Asian (SAS) AF: 0.163 AC: 784 AN: 4814

European-Finnish (FIN) AF: 0.234 AC: 2463 AN: 10544

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14392 AN: 67980

Other (OTH) AF: 0.159 AC: 337 AN: 2114

Alfa AF: 0.193 Hom.: 1582

Bravo AF: 0.138

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.94
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12090554; hg19: chr1-185552348;