rs12623288

Variant names:

• chr2-46407506-G-A
• rs12623288
• ENST00000843945.1:n.122-14312C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-46407506-G-A
• chr2-46407506-G-C

Variant summary

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

The ENST00000843945.1(LINC01820):​n.122-14312C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,170 control chromosomes in the GnomAD database, including 5,794 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 0.22 (5794 hom., cov: 33)
• Consequence: LINC01820 ENST00000843945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 5 publications found

Genes affected

LINC01820 (HGNC:52625): (long intergenic non-protein coding RNA 1820)

LOC124907762 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907762	XR_007086306.1	n.3363-1281C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01820	ENST00000843945.1	n.122-14312C>T		intron_variant	Intron 1 of 2
LINC01820	ENST00000843946.1	n.113-14161C>T		intron_variant	Intron 1 of 2
LINC01820	ENST00000843948.1	n.102+21476C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33050 AN: 152052 Hom.: 5756 Cov.: 33

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0746

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.218 AC: 33138 AN: 152170 Hom.: 5794 Cov.: 33 AF XY: 0.219 AC XY: 16297 AN XY: 74380

African (AFR) AF: 0.437 AC: 18144 AN: 41486

American (AMR) AF: 0.184 AC: 2813 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0746 AC: 259 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3174 AN: 5154

South Asian (SAS) AF: 0.147 AC: 710 AN: 4824

European-Finnish (FIN) AF: 0.126 AC: 1332 AN: 10598

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0878 AC: 5974 AN: 68014

Other (OTH) AF: 0.205 AC: 433 AN: 2112

Alfa AF: 0.138 Hom.: 10314

Bravo AF: 0.239

Asia WGS AF: 0.377 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.66
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs12623288; hg19: chr2-46634645;