rs1160542

chr2-100215693-G-Achr2-100215693-G-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+6873G>A 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 0.454 in 152,056 control chromosomes in the GnomAD database, including 16,975 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 0.45 (16975 hom., cov: 32)
• Consequence: LINC01104 NR_103730.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01104	NR_103730.1	n.567+6873G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01104	ENST00000452354.5	n.567+6873G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68987 AN: 151938 Hom.: 16972 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.454 AC: 69021 AN: 152056 Hom.: 16975 Cov.: 32 AF XY: 0.455 AC XY: 33788 AN XY: 74312

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.466

Alfa AF: 0.505 Hom.: 12135

Bravo AF: 0.435

Asia WGS AF: 0.462 AC: 1605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.22
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1160542; hg19: chr2-100832155;