rs17371334

chr13-84458192-T-G

Variant summary

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

The NR_046871.1(LINC00333):n.139-104172T>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 0.303 in 152,046 control chromosomes in the GnomAD database, including 7,329 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 0.30 (7329 hom., cov: 33)
• Consequence: LINC00333 NR_046871.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

LINC00333 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00333	NR_046871.1	n.139-104172T>G		intron_variant, non_coding_transcript_variant
LOC105370289	XR_942134.1	n.366-46273A>C		intron_variant, non_coding_transcript_variant
LOC105370289	XR_942133.1	n.369-46273A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45997 AN: 151926 Hom.: 7323 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.303 AC: 46004 AN: 152046 Hom.: 7329 Cov.: 33 AF XY: 0.294 AC XY: 21843 AN XY: 74326

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.316

Alfa AF: 0.337 Hom.: 16785

Bravo AF: 0.315

Asia WGS AF: 0.174 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.91
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17371334; hg19: chr13-85032327;