rs2278026

chr16-49398913-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

LOC105371244 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
C16orf78	NM_144602.4	c.651-218C>T		intron_variant		ENST00000299191.4
LOC105371244	XR_001752167.2	n.1812+10436G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C16orf78	ENST00000299191.4	c.651-218C>T		intron_variant		1	NM_144602.4	P1

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

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.173

Alfa AF: 0.173 Hom.: 1071

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

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: rs2278026; hg19: chr16-49432824;