rs10889990

Variant names:

• chr1-72779485-G-A
• rs10889990
• ENST00000418078.3:n.409-622G>A

Variant summary

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

The ENST00000445976.1(ENSG00000225087):​n.281-30209C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 152,070 control chromosomes in the GnomAD database, including 1,492 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 0.083 (1492 hom., cov: 32)
• Consequence: ENSG00000225087 ENST00000445976.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 2 publications found

Genes affected

LINC02796 (HGNC:27918): (long intergenic non-protein coding RNA 2796)

ENSG00000225087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445976.1. 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
	LINC02796	NR_187240.1		n.551+1128G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02796	ENST00000418078.3	TSL:5	n.409-622G>A		intron	N/A
	ENSG00000225087	ENST00000445976.1	TSL:3	n.281-30209C>T		intron	N/A
	ENSG00000225087	ENST00000654386.1		n.326-30209C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12616 AN: 151952 Hom.: 1476 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.00887

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0833 AC: 12670 AN: 152070 Hom.: 1492 Cov.: 32 AF XY: 0.0798 AC XY: 5929 AN XY: 74342

African (AFR) AF: 0.267 AC: 11065 AN: 41426

American (AMR) AF: 0.0352 AC: 538 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3468

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5172

South Asian (SAS) AF: 0.00684 AC: 33 AN: 4824

European-Finnish (FIN) AF: 0.00887 AC: 94 AN: 10596

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0104 AC: 706 AN: 68004

Other (OTH) AF: 0.0659 AC: 139 AN: 2108

Alfa AF: 0.0278 Hom.: 578

Bravo AF: 0.0946

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10889990; hg19: chr1-73245168;