chr12-47370650-G-A

Variant names:

• chr12-47370650-G-A
• rs215389
• NR_183615.1:n.1162G>A

Variant summary

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

The NR_183615.1(LINC02416):​n.1162G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,166 control chromosomes in the GnomAD database, including 2,840 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 0.18 (2840 hom., cov: 33)
• Consequence: LINC02416 NR_183615.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 10 publications found

Genes affected

LINC02416 (HGNC:53345): (long intergenic non-protein coding RNA 2416)

ENSG00000310242 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02416	NR_183615.1	n.1162G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02416	ENST00000718403.1	n.308+3226G>A		intron_variant	Intron 2 of 2
LINC02416	ENST00000718404.1	n.93+16768G>A		intron_variant	Intron 1 of 1
ENSG00000310242	ENST00000848519.1	n.157+15064C>T		intron_variant	Intron 1 of 1
ENSG00000310242	ENST00000848520.1	n.135+15064C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27249 AN: 152048 Hom.: 2844 Cov.: 33

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.179 AC: 27240 AN: 152166 Hom.: 2840 Cov.: 33 AF XY: 0.180 AC XY: 13424 AN XY: 74386

African (AFR) AF: 0.0699 AC: 2905 AN: 41532

American (AMR) AF: 0.148 AC: 2268 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1535 AN: 5174

South Asian (SAS) AF: 0.297 AC: 1432 AN: 4828

European-Finnish (FIN) AF: 0.220 AC: 2324 AN: 10564

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

European-Non Finnish (NFE) AF: 0.224 AC: 15254 AN: 67992

Other (OTH) AF: 0.188 AC: 397 AN: 2114

Alfa AF: 0.198 Hom.: 6156

Bravo AF: 0.165

Asia WGS AF: 0.248 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.48
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs215389; hg19: chr12-47764433;