rs7630522

Positions:

• chr3-107434241-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110039.1(LINC01990):​n.29+3283T>C variant causes a intron, non coding transcript 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 NR_110039.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01990	NR_110039.1	n.29+3283T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01990	ENST00000609293.2	n.67+3283T>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.0691

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.634

Alfa AF: 0.746 Hom.: 69340

Bravo AF: 0.589

Asia WGS AF: 0.337 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7630522; hg19: chr3-107153088;