12-63319341-T-C

Position:

• chr12-63319341-T-C

Variant summary

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

The ENST00000551729.2(LINC03056):​n.163-26405A>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 0.528 in 152,036 control chromosomes in the GnomAD database, including 21,374 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 0.53 (21374 hom., cov: 32)
• Consequence: LINC03056 ENST00000551729.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

LINC03056 (HGNC:56354): (long intergenic non-protein coding RNA 3056)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03056	XR_007063344.1	n.197-26405A>G		intron_variant, non_coding_transcript_variant
LINC03056	XR_007063343.1	n.197-26405A>G		intron_variant, non_coding_transcript_variant
LINC03056	XR_007063345.1	n.45-26405A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03056	ENST00000551729.2	n.163-26405A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80186 AN: 151918 Hom.: 21368 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.528 AC: 80223 AN: 152036 Hom.: 21374 Cov.: 32 AF XY: 0.525 AC XY: 39020 AN XY: 74306

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.528

Alfa AF: 0.526 Hom.: 9209

Bravo AF: 0.527

Asia WGS AF: 0.355 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1146114; hg19: chr12-63713121;