12-8357867-T-C

Variant names:

• chr12-8357867-T-C
• rs12830720
• ENST00000420040.2:n.484-726A>G

Variant summary

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

The ENST00000420040.2(LINC00937):​n.484-726A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 151,958 control chromosomes in the GnomAD database, including 1,694 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 0.13 (1694 hom., cov: 33)
• Consequence: LINC00937 ENST00000420040.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 0 publications found

Genes affected

LINC00937 (HGNC:48629): (long intergenic non-protein coding RNA 937)

LINC02449 (HGNC:53381): (long intergenic non-protein coding RNA 2449)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00937	NR_024420.1	n.484-726A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00937	ENST00000420040.2	n.484-726A>G		intron_variant	Intron 1 of 1	1
LINC00937	ENST00000537659.5	n.446-726A>G		intron_variant	Intron 3 of 3	3
LINC02449	ENST00000537764.2	n.165-11115T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20212 AN: 151838 Hom.: 1693 Cov.: 33

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0661

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.133 AC: 20211 AN: 151958 Hom.: 1694 Cov.: 33 AF XY: 0.131 AC XY: 9747 AN XY: 74306

African (AFR) AF: 0.0476 AC: 1975 AN: 41504

American (AMR) AF: 0.103 AC: 1574 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3466

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5170

South Asian (SAS) AF: 0.0665 AC: 321 AN: 4824

European-Finnish (FIN) AF: 0.187 AC: 1978 AN: 10560

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13186 AN: 67856

Other (OTH) AF: 0.137 AC: 289 AN: 2110

Alfa AF: 0.148 Hom.: 281

Bravo AF: 0.125

Asia WGS AF: 0.0360 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.14
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs12830720; hg19: chr12-8510463;