rs7630522

Variant names:

• chr3-107434241-T-C
• rs7630522
• ENST00000609293.2:n.67+3283T>C

Variant summary

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

The ENST00000609293.2(LINC01990):​n.67+3283T>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 152,114 control chromosomes in the GnomAD database, including 31,444 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 (31444 hom., cov: 32)
• Consequence: LINC01990 ENST00000609293.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 8 publications found

Genes affected

LINC01990 (HGNC:52822): (long intergenic non-protein coding RNA 1990)

DUBR (HGNC:48569): (DPPA2 upstream binding RNA) Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II; positive regulation of myoblast differentiation; and regulation of DNA methylation. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609293.2. 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
	LINC01990	NR_110039.1		n.29+3283T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01990	ENST00000609293.2	TSL:1	n.67+3283T>C		intron	N/A
	LINC01990	ENST00000658914.1		n.204+1038T>C		intron	N/A
	LINC01990	ENST00000664038.1		n.198+1038T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.612 AC: 93038 AN: 151996 Hom.: 31434 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.0695

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.612 AC: 93082 AN: 152114 Hom.: 31444 Cov.: 32 AF XY: 0.605 AC XY: 44952 AN XY: 74348

African (AFR) AF: 0.405 AC: 16808 AN: 41488

American (AMR) AF: 0.536 AC: 8190 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2760 AN: 3470

East Asian (EAS) AF: 0.0691 AC: 357 AN: 5170

South Asian (SAS) AF: 0.596 AC: 2870 AN: 4814

European-Finnish (FIN) AF: 0.668 AC: 7071 AN: 10580

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52590 AN: 68000

Other (OTH) AF: 0.634 AC: 1338 AN: 2112

Alfa AF: 0.720 Hom.: 154815

Bravo AF: 0.589

Asia WGS AF: 0.337 AC: 1175 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	2.4
DANN	Benign	0.50
PhyloP100		0.29

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: rs7630522;

hg19: chr3-107153088;