chr2-100219272-A-G

Variant names:

• chr2-100219272-A-G
• rs10865035
• ENST00000452354.5:n.567+10452A>G

Variant summary

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

The ENST00000452354.5(LINC01104):​n.567+10452A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,122 control chromosomes in the GnomAD database, including 15,708 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 0.43 (15708 hom., cov: 32)
• Consequence: LINC01104 ENST00000452354.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 56 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 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.567+10452A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01104	ENST00000452354.5	TSL:1	n.567+10452A>G		intron	N/A
	LINC01104	ENST00000841887.1		n.669+10452A>G		intron	N/A
	LINC01104	ENST00000841888.1		n.605+10452A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65060 AN: 152006 Hom.: 15704 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.428 AC: 65095 AN: 152122 Hom.: 15708 Cov.: 32 AF XY: 0.430 AC XY: 31958 AN XY: 74380

African (AFR) AF: 0.207 AC: 8601 AN: 41506

American (AMR) AF: 0.392 AC: 5999 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1939 AN: 3464

East Asian (EAS) AF: 0.601 AC: 3105 AN: 5166

South Asian (SAS) AF: 0.409 AC: 1968 AN: 4812

European-Finnish (FIN) AF: 0.566 AC: 5986 AN: 10570

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36006 AN: 67984

Other (OTH) AF: 0.444 AC: 938 AN: 2112

Alfa AF: 0.499 Hom.: 60285

Bravo AF: 0.405

Asia WGS AF: 0.453 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.4
DANN	Benign	0.79
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs10865035; hg19: chr2-100835734;