chr12-131352932-A-C

Position:

• chr12-131352932-A-C

Variant summary

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

The ENST00000659569.1(ENSG00000287792):​n.496T>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 0.356 in 151,906 control chromosomes in the GnomAD database, including 9,754 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 0.36 (9754 hom., cov: 34)
• Consequence: ENST00000659569.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

Genes affected

(HGNC:):

LINC02370 (HGNC:27885): (long intergenic non-protein coding RNA 2370)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02370	NR_103736.1	n.409+3388A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000659569.1	n.496T>G		non_coding_transcript_exon_variant	3/3
LINC02370	ENST00000428272.4	n.409+3388A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54031 AN: 151788 Hom.: 9747 Cov.: 34

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.356 AC: 54055 AN: 151906 Hom.: 9754 Cov.: 34 AF XY: 0.355 AC XY: 26384 AN XY: 74282

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.377

Alfa AF: 0.335 Hom.: 1238

Bravo AF: 0.366

Asia WGS AF: 0.384 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	2.4
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4255618; hg19: chr12-131837477;