rs16935279

chr8-68961217-T-C

Variant summary

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

The NR_039986.1(LINC01592):n.416-7055A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 152,292 control chromosomes in the GnomAD database, including 163 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 0.022 (163 hom., cov: 32)
• Consequence: LINC01592 NR_039986.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

Genes affected

LINC01592 (HGNC:51557): (long intergenic non-protein coding RNA 1592)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01592	NR_039986.1	n.416-7055A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01592	ENST00000518540.5	n.416-7055A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0224 AC: 3408 AN: 152174 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.00519

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0159

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0224 AC: 3407 AN: 152292 Hom.: 163 Cov.: 32 AF XY: 0.0255 AC XY: 1902 AN XY: 74458

Gnomad4 AFR AF: 0.00522

Gnomad4 AMR AF: 0.0161

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0336

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.0250

Alfa AF: 0.0152 Hom.: 9

Bravo AF: 0.0192

Asia WGS AF: 0.152 AC: 526 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	9.6
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16935279; hg19: chr8-69873452;