rs12428824

chr13-75240742-T-C

Variant summary

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

The NR_132375.1(LINC01078):n.55+100T>C 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 0.163 in 152,242 control chromosomes in the GnomAD database, including 2,047 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 0.16 (2047 hom., cov: 32)
• Consequence: LINC01078 NR_132375.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

LINC01078 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01078	NR_132375.1	n.55+100T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24748 AN: 152124 Hom.: 2045 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.163 AC: 24759 AN: 152242 Hom.: 2047 Cov.: 32 AF XY: 0.164 AC XY: 12176 AN XY: 74444

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.182

Alfa AF: 0.159 Hom.: 240

Bravo AF: 0.166

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	12
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12428824; hg19: chr13-75814878;