rs7205278

Positions:

• chr16-29743362-T-C

Variant summary

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

The NM_175900.4(C16orf54):​c.*915A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,774 control chromosomes in the GnomAD database, including 6,850 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 0.26 (6850 hom., cov: 31)
  • Exomes 𝑓: 0.22 (0 hom.)
• Consequence: C16orf54 NM_175900.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

Genes affected

C16orf54 (HGNC:26649): (chromosome 16 open reading frame 54) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C16orf54	NM_175900.4	c.*915A>G		3_prime_UTR_variant	2/2	ENST00000329410.4
C16orf54	XM_047433977.1	c.*915A>G		3_prime_UTR_variant	2/2
C16orf54	XM_047433978.1	c.*915A>G		3_prime_UTR_variant	2/2
C16orf54	XM_047433979.1	c.*528A>G		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C16orf54	ENST00000329410.4	c.*915A>G		3_prime_UTR_variant	2/2	1	NM_175900.4	P1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39928 AN: 151612 Hom.: 6830 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.217 AC: 10 AN: 46 Hom.: 0 Cov.: 0 AF XY: 0.219 AC XY: 7 AN XY: 32

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.118

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.264 AC: 39983 AN: 151728 Hom.: 6850 Cov.: 31 AF XY: 0.261 AC XY: 19322 AN XY: 74156

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.208

Alfa AF: 0.212 Hom.: 883

Bravo AF: 0.271

Asia WGS AF: 0.129 AC: 447 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	7.1
DANN	Benign	0.69

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: rs7205278; hg19: chr16-29754683;