rs16896059

Variant names:

• chr8-97643709-G-A
• rs16896059
• ENST00000659172.1:n.173C>T

Variant summary

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

The ENST00000659172.1(ENSG00000287654):​n.173C>T 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 0.183 in 152,148 control chromosomes in the GnomAD database, including 2,609 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 0.18 (2609 hom., cov: 32)
• Consequence: ENSG00000287654 ENST00000659172.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788

Genes affected

ENSG00000287654 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287654	ENST00000659172.1	n.173C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27777 AN: 152030 Hom.: 2607 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.183 AC: 27791 AN: 152148 Hom.: 2609 Cov.: 32 AF XY: 0.182 AC XY: 13562 AN XY: 74378

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.195

Alfa AF: 0.190 Hom.: 2890

Bravo AF: 0.182

Asia WGS AF: 0.264 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.71
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16896059; hg19: chr8-98655937;