rs4083242

Positions:

• chr16-86334920-G-A
• chr16-86334920-G-C

Variant summary

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

The NR_024406.1(LINC00917):​n.1484-1013C>T 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 0.353 in 152,010 control chromosomes in the GnomAD database, including 11,674 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 0.35 (11674 hom., cov: 32)
• Consequence: LINC00917 NR_024406.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

LINC00917 (HGNC:48607): (long intergenic non-protein coding RNA 917)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00917	NR_024406.1	n.1484-1013C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00917	ENST00000656700.1	n.1565-1013C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53729 AN: 151892 Hom.: 11674 Cov.: 32

Gnomad AFR AF: 0.0863

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.353 AC: 53735 AN: 152010 Hom.: 11674 Cov.: 32 AF XY: 0.360 AC XY: 26746 AN XY: 74278

Gnomad4 AFR AF: 0.0863

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.378

Alfa AF: 0.397 Hom.: 4026

Bravo AF: 0.332

Asia WGS AF: 0.395 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.044
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4083242; hg19: chr16-86368526;