16-86347578-C-G

Position:

• chr16-86347578-C-G

Variant summary

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

The ENST00000598994.2(LINC00917):​n.1698G>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 0.203 in 152,424 control chromosomes in the GnomAD database, including 3,354 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 0.20 (3351 hom., cov: 33)
  • Exomes 𝑓: 0.19 (3 hom.)
• Consequence: LINC00917 ENST00000598994.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

Genes affected

LINC00917 (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 (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.86347578C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00917	ENST00000598994.2	n.1698G>C		non_coding_transcript_exon_variant	2/2	2
LINC00917	ENST00000595169.6	n.89+1973G>C		intron_variant		2
ENSG00000269826	ENST00000595705.1	n.63+129C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30859 AN: 152102 Hom.: 3349 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.217

GnomAD4 exome AF: 0.191 AC: 39 AN: 204 Hom.: 3 AF XY: 0.182 AC XY: 27 AN XY: 148

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.211

Gnomad4 OTH exome AF: 0.0714

GnomAD4 genome AF: 0.203 AC: 30861 AN: 152220 Hom.: 3351 Cov.: 33 AF XY: 0.204 AC XY: 15163 AN XY: 74430

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.216

Alfa AF: 0.114 Hom.: 204

Bravo AF: 0.212

Asia WGS AF: 0.269 AC: 936 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	5.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11641231; hg19: chr16-86381184;