3-160020666-C-T

Position:

• chr3-160020666-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.18C>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 0.0601 in 456,474 control chromosomes in the GnomAD database, including 3,518 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 0.11 (2626 hom., cov: 32)
  • Exomes 𝑓: 0.033 (892 hom.)
• Consequence: LINC01100 NR_104132.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

Genes affected

LINC01100 (HGNC:49224): (long intergenic non-protein coding RNA 1100)

IL12A-AS1 (HGNC:49094): (IL12A antisense RNA 1)

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 = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01100	NR_104132.1	n.18C>T		non_coding_transcript_exon_variant	1/3
IL12A-AS1	NR_108088.1	n.582+4804G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01100	ENST00000471921.2	n.140C>T		non_coding_transcript_exon_variant	3/5	5
IL12A-AS1	ENST00000497452.5	n.582+4804G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17234 AN: 151942 Hom.: 2611 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.000943

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00825

Gnomad OTH AF: 0.0866

GnomAD3 exomes AF: 0.0554 AC: 7450 AN: 134594 Hom.: 710 AF XY: 0.0445 AC XY: 3259 AN XY: 73282

Gnomad AFR exome AF: 0.364

Gnomad AMR exome AF: 0.138

Gnomad ASJ exome AF: 0.00386

Gnomad EAS exome AF: 0.0811

Gnomad SAS exome AF: 0.00943

Gnomad FIN exome AF: 0.00390

Gnomad NFE exome AF: 0.00850

Gnomad OTH exome AF: 0.0382

GnomAD4 exome AF: 0.0334 AC: 10160 AN: 304414 Hom.: 892 Cov.: 0 AF XY: 0.0274 AC XY: 4747 AN XY: 173340

Gnomad4 AFR exome AF: 0.357

Gnomad4 AMR exome AF: 0.139

Gnomad4 ASJ exome AF: 0.00315

Gnomad4 EAS exome AF: 0.0901

Gnomad4 SAS exome AF: 0.0106

Gnomad4 FIN exome AF: 0.00211

Gnomad4 NFE exome AF: 0.00751

Gnomad4 OTH exome AF: 0.0357

GnomAD4 genome AF: 0.114 AC: 17285 AN: 152060 Hom.: 2626 Cov.: 32 AF XY: 0.109 AC XY: 8130 AN XY: 74338

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.0753

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.000943

Gnomad4 NFE AF: 0.00823

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.0347 Hom.: 583

Bravo AF: 0.137

Asia WGS AF: 0.0590 AC: 206 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	0.88
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6771983; hg19: chr3-159738453; COSMIC: COSV71829494;