rs9653442

chr2-100208905-C-T

Variant summary

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

The NR_103730.1(LINC01104):n.567+85C>T 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 0.462 in 152,142 control chromosomes in the GnomAD database, including 17,297 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 0.46 (17295 hom., cov: 33)
  • Exomes 𝑓: 0.75 (2 hom.)
• Consequence: LINC01104 NR_103730.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

Genes affected

LINC01104 (HGNC:49226): (long intergenic non-protein coding RNA 1104)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01104	NR_103730.1	n.567+85C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01104	ENST00000452354.5	n.567+85C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70268 AN: 152016 Hom.: 17290 Cov.: 33

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.476

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 2 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.462 AC: 70302 AN: 152134 Hom.: 17295 Cov.: 33 AF XY: 0.463 AC XY: 34444 AN XY: 74392

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.476

Alfa AF: 0.526 Hom.: 25812

Bravo AF: 0.445

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.81
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9653442; hg19: chr2-100825367;