chr17-69762865-C-T

Variant names:

• chr17-69762865-C-T
• rs16974356
• ENST00000588185.2:n.320-82575C>T

Variant summary

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

The ENST00000588185.2(LINC01483):​n.320-82575C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,098 control chromosomes in the GnomAD database, including 1,583 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 0.12 (1583 hom., cov: 32)
• Consequence: LINC01483 ENST00000588185.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 3 publications found

Genes affected

LINC01483 (HGNC:51130): (long intergenic non-protein coding RNA 1483)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01483	NR_109971.1	n.317-82575C>T		intron_variant	Intron 3 of 5
LINC01483	NR_109972.1	n.317-82575C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01483	ENST00000588185.2	n.320-82575C>T		intron_variant	Intron 3 of 4	3
LINC01483	ENST00000588501.6	n.414-82575C>T		intron_variant	Intron 4 of 6	5
LINC01483	ENST00000591334.6	n.347-82575C>T		intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18149 AN: 151980 Hom.: 1580 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.119 AC: 18159 AN: 152098 Hom.: 1583 Cov.: 32 AF XY: 0.128 AC XY: 9493 AN XY: 74326

African (AFR) AF: 0.0302 AC: 1255 AN: 41534

American (AMR) AF: 0.177 AC: 2706 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3472

East Asian (EAS) AF: 0.367 AC: 1887 AN: 5146

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4814

European-Finnish (FIN) AF: 0.180 AC: 1905 AN: 10570

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8324 AN: 67968

Other (OTH) AF: 0.119 AC: 252 AN: 2116

Alfa AF: 0.124 Hom.: 239

Bravo AF: 0.114

Asia WGS AF: 0.289 AC: 1001 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.66
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs16974356; hg19: chr17-67759006;