rs2469141

Variant names:

• chr15-66675060-T-C
• rs2469141
• ENST00000558797.1:n.264+6606T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558797.1(LINC01169):​n.264+6606T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,982 control chromosomes in the GnomAD database, including 6,848 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 0.27 (6848 hom., cov: 31)
• Consequence: LINC01169 ENST00000558797.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628
• Publications: 1 publications found

Genes affected

LINC01169 (HGNC:49541): (long intergenic non-protein coding RNA 1169)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01169	NR_110372.1	n.264+6606T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01169	ENST00000558797.1	n.264+6606T>C		intron_variant	Intron 3 of 4	1
LINC01169	ENST00000839031.1	n.267-6530T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40451 AN: 151866 Hom.: 6812 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.267 AC: 40537 AN: 151982 Hom.: 6848 Cov.: 31 AF XY: 0.263 AC XY: 19532 AN XY: 74292

African (AFR) AF: 0.484 AC: 20029 AN: 41416

American (AMR) AF: 0.236 AC: 3608 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 598 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1234 AN: 5160

South Asian (SAS) AF: 0.244 AC: 1173 AN: 4816

European-Finnish (FIN) AF: 0.148 AC: 1560 AN: 10574

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11608 AN: 67966

Other (OTH) AF: 0.247 AC: 519 AN: 2100

Alfa AF: 0.192 Hom.: 4895

Bravo AF: 0.281

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2469141; hg19: chr15-66967398;