rs2278026

Variant names:

• chr16-49398913-C-T
• rs2278026
• NM_144602.4:c.651-218C>T

Variant summary

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

The NM_144602.4(C16orf78):​c.651-218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,006 control chromosomes in the GnomAD database, including 3,223 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 0.20 (3223 hom., cov: 32)
• Consequence: C16orf78 NM_144602.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 2 publications found

Genes affected

C16orf78 (HGNC:28479): (chromosome 16 open reading frame 78) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000262950 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C16orf78	NM_144602.4	c.651-218C>T		intron_variant	Intron 4 of 4	ENST00000299191.4	NP_653203.1
LOC105371244	XR_001752167.2	n.1812+10436G>A		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C16orf78	ENST00000299191.4	c.651-218C>T		intron_variant	Intron 4 of 4	1	NM_144602.4	ENSP00000299191.3
ENSG00000262950	ENST00000849660.1	n.585+10436G>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29786 AN: 151886 Hom.: 3215 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.196 AC: 29820 AN: 152006 Hom.: 3223 Cov.: 32 AF XY: 0.199 AC XY: 14760 AN XY: 74290

African (AFR) AF: 0.272 AC: 11273 AN: 41422

American (AMR) AF: 0.117 AC: 1789 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0905 AC: 314 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1304 AN: 5174

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4816

European-Finnish (FIN) AF: 0.210 AC: 2215 AN: 10548

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10792 AN: 67976

Other (OTH) AF: 0.173 AC: 366 AN: 2110

Alfa AF: 0.174 Hom.: 1256

Bravo AF: 0.189

Asia WGS AF: 0.290 AC: 1007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.64
PhyloP100		-0.90
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: rs2278026; hg19: chr16-49432824;