4-111882716-A-G

Variant names:

• chr4-111882716-A-G
• rs6826919
• ENST00000508010.2:n.195-53666T>C

Variant summary

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

The ENST00000511219.1(LINC02945):​n.135-53666T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,254 control chromosomes in the GnomAD database, including 23,598 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 0.56 (23598 hom., cov: 32)
• Consequence: LINC02945 ENST00000511219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 2 publications found

Genes affected

LINC02945 (HGNC:55960): (long intergenic non-protein coding RNA 2945)

ENSG00000288691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511219.1. 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
	LINC02945	NR_186680.1		n.99-53666T>C		intron	N/A
	LINC02945	NR_186681.1		n.185-53666T>C		intron	N/A
	LINC02945	NR_186682.1		n.83-53666T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02945	ENST00000508010.2	TSL:5	n.195-53666T>C		intron	N/A
	LINC02945	ENST00000511219.1	TSL:3	n.135-53666T>C		intron	N/A
	ENSG00000288691	ENST00000679726.1		n.171-19317A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.556 AC: 83985 AN: 151138 Hom.: 23591 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.555 AC: 84017 AN: 151254 Hom.: 23598 Cov.: 32 AF XY: 0.561 AC XY: 41448 AN XY: 73918

African (AFR) AF: 0.468 AC: 19370 AN: 41400

American (AMR) AF: 0.582 AC: 8789 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2286 AN: 3452

East Asian (EAS) AF: 0.691 AC: 3563 AN: 5160

South Asian (SAS) AF: 0.672 AC: 3234 AN: 4810

European-Finnish (FIN) AF: 0.603 AC: 6354 AN: 10544

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 38781 AN: 67466

Other (OTH) AF: 0.539 AC: 1133 AN: 2102

Alfa AF: 0.575 Hom.: 11382

Bravo AF: 0.549

Asia WGS AF: 0.681 AC: 2351 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.3
DANN	Benign	0.83
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs6826919; hg19: chr4-112803872;