rs12748299

chr1-199014195-C-Gchr1-199014195-C-T

Variant summary

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

The NR_110525.1(LINC01222):n.183+4587G>C 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 0.243 in 152,058 control chromosomes in the GnomAD database, including 5,178 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 (5178 hom., cov: 31)
• Consequence: LINC01222 NR_110525.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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/exons	MANE	UniProt
LINC01222	NR_110525.1	n.183+4587G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01222	ENST00000427439.1	n.221-5627G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36974 AN: 151940 Hom.: 5176 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.243 AC: 36985 AN: 152058 Hom.: 5178 Cov.: 31 AF XY: 0.237 AC XY: 17624 AN XY: 74320

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.0870

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.273

Alfa AF: 0.156 Hom.: 306

Bravo AF: 0.236

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.3
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12748299; hg19: chr1-198983324;