rs7581641

Variant names:

• chr2-8485976-C-T
• rs7581641
• ENST00000655671.1:n.48+2026G>A

Variant summary

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

The ENST00000655671.1(LINC00299):​n.48+2026G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,208 control chromosomes in the GnomAD database, including 1,692 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 0.10 (1692 hom., cov: 32)
• Consequence: LINC00299 ENST00000655671.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.61

Genes affected

LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

LINC01814 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00299	ENST00000655671.1	n.48+2026G>A		intron_variant	Intron 1 of 6
LINC00299	ENST00000661371.1	n.89+2026G>A		intron_variant	Intron 1 of 5
LINC01814	ENST00000670008.1	n.1018-23580G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15363 AN: 152090 Hom.: 1683 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0586

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0270

Gnomad OTH AF: 0.0934

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

GnomAD4 genome AF: 0.101 AC: 15412 AN: 152208 Hom.: 1692 Cov.: 32 AF XY: 0.101 AC XY: 7547 AN XY: 74428

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0586

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.0448

Gnomad4 SAS AF: 0.0923

Gnomad4 FIN AF: 0.0268

Gnomad4 NFE AF: 0.0270

Gnomad4 OTH AF: 0.0986

Alfa AF: 0.0510 Hom.: 254

Bravo AF: 0.109

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.038
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7581641; hg19: chr2-8626106;