16-87148335-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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.111-7232A>G		intron_variant	Intron 1 of 4	2

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

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.403

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6540013; hg19: chr16-87181941;