rs1160542

Variant names:

• chr2-100215693-G-A
• rs1160542
• ENST00000452354.5:n.567+6873G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-100215693-G-A
• chr2-100215693-G-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+6873G>A variant causes a intron 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 ENST00000452354.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 34 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=-0.88).
• 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 rank	MANE	Protein	UniProt
LINC01104	NR_103730.1	n.567+6873G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01104	ENST00000452354.5	n.567+6873G>A		intron_variant	Intron 1 of 2	1
LINC01104	ENST00000841887.1	n.669+6873G>A		intron_variant	Intron 1 of 4
LINC01104	ENST00000841888.1	n.605+6873G>A		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.271 AC: 11233 AN: 41478

American (AMR) AF: 0.411 AC: 6279 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1951 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3145 AN: 5164

South Asian (SAS) AF: 0.420 AC: 2025 AN: 4820

European-Finnish (FIN) AF: 0.568 AC: 5990 AN: 10554

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36858 AN: 67970

Other (OTH) AF: 0.466 AC: 981 AN: 2106

Alfa AF: 0.512 Hom.: 17602

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1160542; hg19: chr2-100832155;