12-8357867-T-C

Position:

• chr12-8357867-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024420.1(LINC00937):​n.484-726A>G variant causes a intron, non coding transcript 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 NR_024420.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC00937	NR_024420.1	n.484-726A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00937	ENST00000420040.2	n.484-726A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000537764.2	n.165-11115T>C		intron_variant, non_coding_transcript_variant		3
LINC00937	ENST00000537659.5	n.446-726A>G		intron_variant, non_coding_transcript_variant		3
LINC00937	ENST00000539348.5	n.269-726A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0665

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.137

Alfa AF: 0.150 Hom.: 278

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12830720; hg19: chr12-8510463;