3-160026651-C-T

Position:

• chr3-160026651-C-T

Variant summary

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

The NR_104132.1(LINC01100):​n.138C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 456,322 control chromosomes in the GnomAD database, including 127,159 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 0.72 (40224 hom., cov: 32)
  • Exomes 𝑓: 0.75 (86935 hom.)
• Consequence: LINC01100 NR_104132.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

LINC01100 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01100	NR_104132.1	n.138C>T		non_coding_transcript_exon_variant	2/3
IL12A-AS1	NR_108088.1	n.518-1117G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01100	ENST00000471921.2	n.260C>T		non_coding_transcript_exon_variant	4/5	5
IL12A-AS1	ENST00000497452.5	n.518-1117G>A		intron_variant		2
IL12A-AS1	ENST00000642756.1	n.366+12259G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109152 AN: 151806 Hom.: 40213 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.937

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.748

GnomAD3 exomes AF: 0.732 AC: 98490 AN: 134520 Hom.: 36668 AF XY: 0.729 AC XY: 53428 AN XY: 73258

Gnomad AFR exome AF: 0.532

Gnomad AMR exome AF: 0.728

Gnomad ASJ exome AF: 0.816

Gnomad EAS exome AF: 0.599

Gnomad SAS exome AF: 0.632

Gnomad FIN exome AF: 0.811

Gnomad NFE exome AF: 0.803

Gnomad OTH exome AF: 0.767

GnomAD4 exome AF: 0.750 AC: 228264 AN: 304398 Hom.: 86935 Cov.: 0 AF XY: 0.741 AC XY: 128387 AN XY: 173332

Gnomad4 AFR exome AF: 0.537

Gnomad4 AMR exome AF: 0.728

Gnomad4 ASJ exome AF: 0.816

Gnomad4 EAS exome AF: 0.603

Gnomad4 SAS exome AF: 0.636

Gnomad4 FIN exome AF: 0.815

Gnomad4 NFE exome AF: 0.808

Gnomad4 OTH exome AF: 0.761

GnomAD4 genome AF: 0.719 AC: 109192 AN: 151924 Hom.: 40224 Cov.: 32 AF XY: 0.719 AC XY: 53368 AN XY: 74242

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.743

Alfa AF: 0.752 Hom.: 8584

Bravo AF: 0.709

Asia WGS AF: 0.575 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2914119; hg19: chr3-159744438;