16-87159478-T-C

Position:

• chr16-87159478-T-C

Variant summary

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

The variant allele was found at a frequency of 0.89 in 152,000 control chromosomes in the GnomAD database, including 60,459 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 0.89 (60459 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.87159478T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C16orf95	ENST00000562840.1	n.111-18375A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135237 AN: 151882 Hom.: 60408 Cov.: 30

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.890 AC: 135341 AN: 152000 Hom.: 60459 Cov.: 30 AF XY: 0.884 AC XY: 65663 AN XY: 74274

Gnomad4 AFR AF: 0.933

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.894

Alfa AF: 0.885 Hom.: 8072

Bravo AF: 0.903

Asia WGS AF: 0.949 AC: 3301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8061121; hg19: chr16-87193084;