rs6538370

Positions:

• chr12-92995154-A-G

Variant summary

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

The XR_945212.3(LINC02413):​n.66+4344A>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 0.387 in 151,980 control chromosomes in the GnomAD database, including 11,698 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 0.39 (11698 hom., cov: 31)
• Consequence: LINC02413 XR_945212.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

Genes affected

LINC02413 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02413	XR_945212.3	n.66+4344A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58734 AN: 151862 Hom.: 11689 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0813

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.387 AC: 58782 AN: 151980 Hom.: 11698 Cov.: 31 AF XY: 0.382 AC XY: 28418 AN XY: 74302

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.0815

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.378

Alfa AF: 0.401 Hom.: 6828

Bravo AF: 0.390

Asia WGS AF: 0.202 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
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: rs6538370; hg19: chr12-93388930;