16-4596877-G-A

Variant names:

• chr16-4596877-G-A
• rs8050907
• NM_001145011.2:c.3127+2074G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145011.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C16orf96	NM_001145011.2	MANE Select	c.3127+2074G>A		intron	N/A	NP_001138483.1
	C16orf96	NM_001387219.1		c.3127+2074G>A		intron	N/A	NP_001374148.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C16orf96	ENST00000444310.5	TSL:5 MANE Select	c.3127+2074G>A		intron	N/A	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

African (AFR) AF: 0.167 AC: 6906 AN: 41462

American (AMR) AF: 0.0453 AC: 693 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.00559 AC: 27 AN: 4828

European-Finnish (FIN) AF: 0.0265 AC: 281 AN: 10596

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0347 AC: 2363 AN: 68010

Other (OTH) AF: 0.0629 AC: 133 AN: 2116

Alfa AF: 0.0741 Hom.: 435

Bravo AF: 0.0769

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.73
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8050907; hg19: chr16-4646878;