NR_132375.1:n.55+100T>C

Variant names:

• chr13-75240742-T-C
• rs12428824
• NR_132375.1:n.55+100T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_132375.1(LINC01078):​n.55+100T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 3 publications found

Genes affected

LINC01078 (HGNC:49121): (long intergenic non-protein coding RNA 1078)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01078	NR_132375.1	n.55+100T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.137 AC: 5706 AN: 41554

American (AMR) AF: 0.211 AC: 3224 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1107 AN: 5178

South Asian (SAS) AF: 0.121 AC: 582 AN: 4820

European-Finnish (FIN) AF: 0.148 AC: 1569 AN: 10604

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11227 AN: 67998

Other (OTH) AF: 0.182 AC: 384 AN: 2114

Alfa AF: 0.157 Hom.: 255

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs12428824; hg19: chr13-75814878;