16-87148335-T-C

Variant names:

• chr16-87148335-T-C
• rs6540013
• ENST00000562840.1:n.111-7232A>G

Variant summary

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

The ENST00000562840.1(C16orf95):​n.111-7232A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,914 control chromosomes in the GnomAD database, including 12,833 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 0.41 (12833 hom., cov: 32)
• Consequence: C16orf95 ENST00000562840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 4 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562840.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C16orf95	ENST00000562840.1	TSL:2	n.111-7232A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62102 AN: 151796 Hom.: 12825 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.409 AC: 62138 AN: 151914 Hom.: 12833 Cov.: 32 AF XY: 0.405 AC XY: 30039 AN XY: 74260

African (AFR) AF: 0.395 AC: 16343 AN: 41420

American (AMR) AF: 0.356 AC: 5436 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1574 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1757 AN: 5170

South Asian (SAS) AF: 0.393 AC: 1886 AN: 4798

European-Finnish (FIN) AF: 0.356 AC: 3755 AN: 10556

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.442 AC: 30025 AN: 67924

Other (OTH) AF: 0.403 AC: 850 AN: 2108

Alfa AF: 0.433 Hom.: 3589

Bravo AF: 0.409

Asia WGS AF: 0.330 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.0
DANN	Benign	0.72
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6540013; hg19: chr16-87181941;