chr9-25828416-C-T

Variant names:

• chr9-25828416-C-T
• rs1220058
• ENST00000665756.1:n.863-15904C>T

Variant summary

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

The ENST00000665756.1(LINC01241):​n.863-15904C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,978 control chromosomes in the GnomAD database, including 19,976 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 0.49 (19976 hom., cov: 31)
• Consequence: LINC01241 ENST00000665756.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

LINC01241 (HGNC:49804): (long intergenic non-protein coding RNA 1241)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 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
LINC01241	ENST00000665756.1	n.863-15904C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73865 AN: 151860 Hom.: 19982 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.486 AC: 73866 AN: 151978 Hom.: 19976 Cov.: 31 AF XY: 0.490 AC XY: 36376 AN XY: 74282

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.512

Alfa AF: 0.552 Hom.: 4892

Bravo AF: 0.469

Asia WGS AF: 0.442 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.7
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1220058; hg19: chr9-25828414; COSMIC: COSV60345778;