16-87159478-T-C

Variant names:

• chr16-87159478-T-C
• rs8061121
• ENST00000562840.1:n.111-18375A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000562840.1(C16orf95):​n.111-18375A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: C16orf95 ENST00000562840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 8 publications found

Genes affected

C16orf95 (HGNC:40033): (chromosome 16 open reading frame 95)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C16orf95	ENST00000562840.1	n.111-18375A>G		intron_variant	Intron 1 of 4	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

African (AFR) AF: 0.933 AC: 38684 AN: 41476

American (AMR) AF: 0.897 AC: 13687 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3053 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5164 AN: 5172

South Asian (SAS) AF: 0.904 AC: 4338 AN: 4800

European-Finnish (FIN) AF: 0.771 AC: 8118 AN: 10534

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59374 AN: 67966

Other (OTH) AF: 0.894 AC: 1888 AN: 2112

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs8061121; hg19: chr16-87193084;