chr1-199014195-C-G

Variant names:

• chr1-199014195-C-G
• rs12748299
• ENST00000427439.1:n.221-5627G>C

Variant summary

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

The ENST00000427439.1(LINC01222):​n.221-5627G>C variant causes a intron 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 ENST00000427439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• 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=-0.84).
• 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 rank	MANE	Protein	UniProt
LINC01222	NR_110525.1	n.183+4587G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01222	ENST00000427439.1	n.221-5627G>C		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.136 AC: 5658 AN: 41490

American (AMR) AF: 0.212 AC: 3241 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3468

East Asian (EAS) AF: 0.142 AC: 735 AN: 5162

South Asian (SAS) AF: 0.0870 AC: 419 AN: 4818

European-Finnish (FIN) AF: 0.297 AC: 3142 AN: 10572

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21851 AN: 67976

Other (OTH) AF: 0.273 AC: 574 AN: 2106

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs12748299; hg19: chr1-198983324;