rs10805066

Variant names:

• chr4-73726673-G-C
• rs10805066
• ENST00000821867.1:n.160-7830G>C

Your query was ambiguous. Multiple possible variants found:

• chr4-73726673-G-C
• chr4-73726673-G-T

Variant summary

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

The ENST00000821867.1(UMLILO):​n.160-7830G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,952 control chromosomes in the GnomAD database, including 29,708 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 0.61 (29708 hom., cov: 31)
• Consequence: UMLILO ENST00000821867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 6 publications found

Genes affected

UMLILO (HGNC:51824): (upstream master lncRNA of the inflammatory chemokine locus)

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 = 0.854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821867.1. 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
	UMLILO	ENST00000821867.1		n.160-7830G>C		intron	N/A
	UMLILO	ENST00000821868.1		n.176-7830G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92933 AN: 151834 Hom.: 29691 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.612 AC: 92971 AN: 151952 Hom.: 29708 Cov.: 31 AF XY: 0.619 AC XY: 45995 AN XY: 74260

African (AFR) AF: 0.423 AC: 17509 AN: 41434

American (AMR) AF: 0.714 AC: 10896 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2446 AN: 3470

East Asian (EAS) AF: 0.875 AC: 4501 AN: 5142

South Asian (SAS) AF: 0.745 AC: 3587 AN: 4814

European-Finnish (FIN) AF: 0.687 AC: 7242 AN: 10542

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.657 AC: 44664 AN: 67966

Other (OTH) AF: 0.640 AC: 1353 AN: 2114

Alfa AF: 0.641 Hom.: 3794

Bravo AF: 0.607

Asia WGS AF: 0.793 AC: 2756 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	0.35
DANN	Benign	0.54
PhyloP100		-0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10805066;

hg19: chr4-74592390;