chr2-100254400-T-C

Variant names:

• chr2-100254400-T-C
• rs4851274
• ENST00000841887.1:n.*222T>C

Variant summary

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

The ENST00000841887.1(LINC01104):​n.*222T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,004 control chromosomes in the GnomAD database, including 32,286 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 (32286 hom., cov: 31)
• Consequence: LINC01104 ENST00000841887.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 11 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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841887.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01104	ENST00000841887.1		n.*222T>C		downstream_gene	N/A
	LINC01104	ENST00000841888.1		n.*224T>C		downstream_gene	N/A
	LINC01104	ENST00000841889.1		n.*218T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98273 AN: 151888 Hom.: 32253 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.647 AC: 98359 AN: 152004 Hom.: 32286 Cov.: 31 AF XY: 0.647 AC XY: 48034 AN XY: 74296

African (AFR) AF: 0.639 AC: 26484 AN: 41420

American (AMR) AF: 0.512 AC: 7824 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2291 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3349 AN: 5148

South Asian (SAS) AF: 0.543 AC: 2614 AN: 4818

European-Finnish (FIN) AF: 0.729 AC: 7717 AN: 10582

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46069 AN: 67958

Other (OTH) AF: 0.608 AC: 1286 AN: 2116

Alfa AF: 0.662 Hom.: 140999

Bravo AF: 0.631

Asia WGS AF: 0.568 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.17
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4851274; hg19: chr2-100870862;