chr2-100208905-C-T

Variant names:

• chr2-100208905-C-T
• rs9653442
• ENST00000452354.5:n.567+85C>T

Variant summary

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

The ENST00000452354.5(LINC01104):​n.567+85C>T variant causes a intron 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 ENST00000452354.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 77 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452354.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01104	NR_103730.1		n.567+85C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01104	ENST00000452354.5	TSL:1	n.567+85C>T		intron	N/A
	LINC01104	ENST00000841887.1		n.669+85C>T		intron	N/A
	LINC01104	ENST00000841888.1		n.605+85C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 4 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.306 AC: 12692 AN: 41498

American (AMR) AF: 0.414 AC: 6323 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1930 AN: 3470

East Asian (EAS) AF: 0.610 AC: 3154 AN: 5170

South Asian (SAS) AF: 0.415 AC: 2003 AN: 4822

European-Finnish (FIN) AF: 0.568 AC: 6019 AN: 10594

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36617 AN: 67986

Other (OTH) AF: 0.476 AC: 1004 AN: 2110

Alfa AF: 0.514 Hom.: 62192

Bravo AF: 0.445

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.46
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs9653442; hg19: chr2-100825367;