rs7659755

Positions:

• chr4-181087979-G-A

Variant summary

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

The NR_033918.1(LINC00290):​n.202-23499C>T 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 0.795 in 152,092 control chromosomes in the GnomAD database, including 48,391 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 0.79 (48391 hom., cov: 32)
• Consequence: LINC00290 NR_033918.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

LINC00290 (HGNC:38515): (long intergenic non-protein coding RNA 290)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00290	NR_033918.1	n.202-23499C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00290	ENST00000512487.1	n.202-23499C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120828 AN: 151974 Hom.: 48370 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.795 AC: 120900 AN: 152092 Hom.: 48391 Cov.: 32 AF XY: 0.796 AC XY: 59170 AN XY: 74338

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.816

Alfa AF: 0.814 Hom.: 101867

Bravo AF: 0.790

Asia WGS AF: 0.877 AC: 3053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7659755; hg19: chr4-182009132;