chr2-100236725-G-A

Variant names:

• chr2-100236725-G-A
• rs7597861
• ENST00000452354.5:n.568-10387G>A

Variant summary

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

The ENST00000452354.5(LINC01104):​n.568-10387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,092 control chromosomes in the GnomAD database, including 32,367 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 0.65 (32367 hom., cov: 32)
• Consequence: LINC01104 ENST00000452354.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 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.568-10387G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01104	ENST00000452354.5	TSL:1	n.568-10387G>A		intron	N/A
	LINC01104	ENST00000841887.1		n.670-10387G>A		intron	N/A
	LINC01104	ENST00000841888.1		n.606-10387G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98488 AN: 151974 Hom.: 32333 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.648 AC: 98576 AN: 152092 Hom.: 32367 Cov.: 32 AF XY: 0.648 AC XY: 48203 AN XY: 74352

African (AFR) AF: 0.667 AC: 27675 AN: 41480

American (AMR) AF: 0.510 AC: 7804 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2314 AN: 3472

East Asian (EAS) AF: 0.649 AC: 3346 AN: 5152

South Asian (SAS) AF: 0.559 AC: 2695 AN: 4822

European-Finnish (FIN) AF: 0.718 AC: 7598 AN: 10580

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45133 AN: 67982

Other (OTH) AF: 0.609 AC: 1285 AN: 2110

Alfa AF: 0.652 Hom.: 4033

Bravo AF: 0.633

Asia WGS AF: 0.574 AC: 1999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.52
DANN	Benign	0.22
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs7597861; hg19: chr2-100853187;