16-87148335-T-C

Position:

• chr16-87148335-T-C

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C16orf95	ENST00000562840.1	n.111-7232A>G		intron_variant, non_coding_transcript_variant		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;