12-126874646-T-C

Variant names:

• chr12-126874646-T-C
• rs7970012
• ENST00000507482.7:n.49A>G

Variant summary

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

The ENST00000507482.7(LINC02372):​n.49A>G 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 0.237 in 152,262 control chromosomes in the GnomAD database, including 5,420 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 (5418 hom., cov: 32)
  • Exomes 𝑓: 0.25 (2 hom.)
• Consequence: LINC02372 ENST00000507482.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 6 publications found

Genes affected

LINC02372 (HGNC:53294): (long intergenic non-protein coding RNA 2372)

ENSG00000256286 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02372	NR_033970.1	n.45A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105370061	XR_001749174.2	n.-158T>C		upstream_gene_variant
LOC105370061	XR_007063516.1	n.-158T>C		upstream_gene_variant
LOC105370061	XR_945511.3	n.-158T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02372	ENST00000507482.7	n.49A>G		non_coding_transcript_exon_variant	Exon 1 of 3	1
LINC02372	ENST00000541348.2	n.26A>G		non_coding_transcript_exon_variant	Exon 1 of 3	3
LINC02372	ENST00000544727.3	n.71A>G		non_coding_transcript_exon_variant	Exon 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36104 AN: 152108 Hom.: 5418 Cov.: 32

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.276

GnomAD4 exome AF: 0.250 AC: 9 AN: 36 Hom.: 2 Cov.: 0 AF XY: 0.267 AC XY: 8 AN XY: 30

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.214 AC: 6 AN: 28

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.237 AC: 36093 AN: 152226 Hom.: 5418 Cov.: 32 AF XY: 0.237 AC XY: 17631 AN XY: 74424

African (AFR) AF: 0.0784 AC: 3257 AN: 41556

American (AMR) AF: 0.238 AC: 3632 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5178

South Asian (SAS) AF: 0.316 AC: 1527 AN: 4828

European-Finnish (FIN) AF: 0.308 AC: 3262 AN: 10594

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22594 AN: 68000

Other (OTH) AF: 0.272 AC: 575 AN: 2112

Alfa AF: 0.301 Hom.: 9165

Bravo AF: 0.221

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.5
DANN	Benign	0.41
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7970012; hg19: chr12-127359192;