chr2-100221105-T-C

Variant names:

• chr2-100221105-T-C
• rs2309837
• ENST00000452354.5:n.567+12285T>C

Variant summary

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

The ENST00000452354.5(LINC01104):​n.567+12285T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,092 control chromosomes in the GnomAD database, including 23,336 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 0.55 (23336 hom., cov: 32)
• Consequence: LINC01104 ENST00000452354.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94
• Publications: 9 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01104	NR_103730.1	n.567+12285T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01104	ENST00000452354.5	n.567+12285T>C		intron_variant	Intron 1 of 2	1
LINC01104	ENST00000841887.1	n.669+12285T>C		intron_variant	Intron 1 of 4
LINC01104	ENST00000841888.1	n.605+12285T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82967 AN: 151974 Hom.: 23321 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.530

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.546 AC: 83027 AN: 152092 Hom.: 23336 Cov.: 32 AF XY: 0.547 AC XY: 40686 AN XY: 74350

African (AFR) AF: 0.445 AC: 18473 AN: 41470

American (AMR) AF: 0.454 AC: 6933 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3470

East Asian (EAS) AF: 0.609 AC: 3150 AN: 5170

South Asian (SAS) AF: 0.478 AC: 2299 AN: 4814

European-Finnish (FIN) AF: 0.677 AC: 7168 AN: 10584

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41168 AN: 67984

Other (OTH) AF: 0.529 AC: 1118 AN: 2112

Alfa AF: 0.585 Hom.: 14426

Bravo AF: 0.526

Asia WGS AF: 0.497 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.022
DANN	Benign	0.41
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs2309837; hg19: chr2-100837567;