7-127480443-C-G

Position:

• chr7-127480443-C-G

Variant summary

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

The NR_110024.1(LINC03012):​n.264+1206C>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 0.268 in 152,108 control chromosomes in the GnomAD database, including 7,191 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 0.27 (7191 hom., cov: 32)
• Consequence: LINC03012 NR_110024.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

Genes affected

LINC03012 (HGNC:56139): (long intergenic non-protein coding RNA 3012)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03012	NR_110024.1	n.264+1206C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03012	ENST00000448311.1	n.264+1206C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40815 AN: 151990 Hom.: 7186 Cov.: 32

Gnomad AFR AF: 0.0658

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.268 AC: 40818 AN: 152108 Hom.: 7191 Cov.: 32 AF XY: 0.277 AC XY: 20599 AN XY: 74340

Gnomad4 AFR AF: 0.0656

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.262

Alfa AF: 0.299 Hom.: 1087

Bravo AF: 0.252

Asia WGS AF: 0.449 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1419410; hg19: chr7-127120497;