rs2309837

Positions:

• chr2-100221105-T-C

Variant summary

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

The NR_103730.1(LINC01104):​n.567+12285T>C 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 0.546 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 NR_103730.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94

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=-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/exons	MANE	UniProt
LINC01104	NR_103730.1	n.567+12285T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01104	ENST00000452354.5	n.567+12285T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.529

Alfa AF: 0.579 Hom.: 8959

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2309837; hg19: chr2-100837567;