rs8050907

Positions:

• chr16-4596877-G-A

Variant summary

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

The NM_001145011.2(C16orf96):​c.3127+2074G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0697 in 152,158 control chromosomes in the GnomAD database, including 685 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 0.070 (685 hom., cov: 33)
• Consequence: C16orf96 NM_001145011.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735

Genes affected

C16orf96 (HGNC:40031): (chromosome 16 open reading frame 96)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C16orf96	NM_001145011.2	c.3127+2074G>A		intron_variant		ENST00000444310.5	NP_001138483.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C16orf96	ENST00000444310.5	c.3127+2074G>A		intron_variant		5	NM_001145011.2	ENSP00000415027.3

Frequencies

GnomAD3 genomes AF: 0.0697 AC: 10602 AN: 152042 Hom.: 685 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0454

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.00600

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0697 AC: 10612 AN: 152158 Hom.: 685 Cov.: 33 AF XY: 0.0672 AC XY: 5003 AN XY: 74406

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.0453

Gnomad4 ASJ AF: 0.0550

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.00559

Gnomad4 FIN AF: 0.0265

Gnomad4 NFE AF: 0.0347

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0517 Hom.: 114

Bravo AF: 0.0769

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs8050907; hg19: chr16-4646878;