16-86331965-C-G

Position:

• chr16-86331965-C-G

Variant summary

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

The NR_024406.1(LINC00917):​n.2503G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.982 in 152,366 control chromosomes in the GnomAD database, including 73,529 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 0.98 (73521 hom., cov: 32)
  • Exomes 𝑓: 1.0 (8 hom.)
• Consequence: LINC00917 NR_024406.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00917	NR_024406.1	n.2503G>C		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00917	ENST00000656700.1	n.2584G>C		non_coding_transcript_exon_variant	8/8

Frequencies

GnomAD3 genomes AF: 0.982 AC: 149551 AN: 152232 Hom.: 73464 Cov.: 32

Gnomad AFR AF: 0.995

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.987

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.982

GnomAD4 exome AF: 1.00 AC: 16 AN: 16 Hom.: 8 Cov.: 0 AF XY: 1.00 AC XY: 12 AN XY: 12

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.982 AC: 149667 AN: 152350 Hom.: 73521 Cov.: 32 AF XY: 0.984 AC XY: 73270 AN XY: 74498

Gnomad4 AFR AF: 0.995

Gnomad4 AMR AF: 0.987

Gnomad4 ASJ AF: 0.979

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.983

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.983

Alfa AF: 0.976 Hom.: 40130

Bravo AF: 0.983

Asia WGS AF: 0.993 AC: 3453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.88
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2696835; hg19: chr16-86365571;