chr1-199012112-T-C

Variant names:

• chr1-199012112-T-C
• rs12757682
• ENST00000427439.1:n.221-3544A>G

Variant summary

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

The ENST00000427439.1(LINC01222):​n.221-3544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,024 control chromosomes in the GnomAD database, including 5,142 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 0.24 (5142 hom., cov: 31)
• Consequence: LINC01222 ENST00000427439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 5 publications found

Genes affected

LINC01222 (HGNC:49672): (long intergenic non-protein coding RNA 1222)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01222	NR_110525.1	n.184-3544A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01222	ENST00000427439.1	n.221-3544A>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36734 AN: 151906 Hom.: 5140 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.242 AC: 36745 AN: 152024 Hom.: 5142 Cov.: 31 AF XY: 0.235 AC XY: 17481 AN XY: 74292

African (AFR) AF: 0.136 AC: 5645 AN: 41510

American (AMR) AF: 0.213 AC: 3244 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3466

East Asian (EAS) AF: 0.105 AC: 543 AN: 5184

South Asian (SAS) AF: 0.0877 AC: 423 AN: 4824

European-Finnish (FIN) AF: 0.297 AC: 3140 AN: 10556

Middle Eastern (MID) AF: 0.279 AC: 81 AN: 290

European-Non Finnish (NFE) AF: 0.321 AC: 21809 AN: 67916

Other (OTH) AF: 0.272 AC: 573 AN: 2108

Alfa AF: 0.298 Hom.: 11072

Bravo AF: 0.234

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.8
DANN	Benign	0.82
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12757682; hg19: chr1-198981241;