rs1220058

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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
LINC01241	ENST00000758796.1	n.467-15904C>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.233 AC: 9663 AN: 41468

American (AMR) AF: 0.574 AC: 8754 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1942 AN: 5136

South Asian (SAS) AF: 0.527 AC: 2536 AN: 4816

European-Finnish (FIN) AF: 0.644 AC: 6807 AN: 10566

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40485 AN: 67944

Other (OTH) AF: 0.512 AC: 1081 AN: 2112

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
PhyloP100		0.30

Splicing

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

Other links and lift over

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