rs16896059

Positions:

• chr8-97643709-G-A

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/exons	MANE	Protein	UniProt
		n.97643709G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287654	ENST00000659172.1	n.173C>T		non_coding_transcript_exon_variant	1/1

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;