17-73242948-G-T

Position:

• chr17-73242948-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001351264.2(C17orf80):​c.1674G>T​(p.Thr558=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 1,613,134 control chromosomes in the GnomAD database, including 101,396 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 0.28 (7276 hom., cov: 32)
  • Exomes 𝑓: 0.35 (94120 hom.)
• Consequence: C17orf80 NM_001351264.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.46

Genes affected

C17orf80 (HGNC:29601): (mitochondrial nucleoid associated protein 1) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

CPSF4L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP7: Synonymous conserved (PhyloP=-3.46 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C17orf80	NM_001351264.2	c.1674G>T	p.Thr558=	synonymous_variant	5/6	ENST00000535032.7	NP_001338193.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C17orf80	ENST00000535032.7	c.1674G>T	p.Thr558=	synonymous_variant	5/6	1	NM_001351264.2	ENSP00000440551	A2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42791 AN: 151934 Hom.: 7280 Cov.: 32

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.304

GnomAD3 exomes AF: 0.325 AC: 81595 AN: 250688 Hom.: 14198 AF XY: 0.327 AC XY: 44273 AN XY: 135498

Gnomad AFR exome AF: 0.0823

Gnomad AMR exome AF: 0.378

Gnomad ASJ exome AF: 0.382

Gnomad EAS exome AF: 0.185

Gnomad SAS exome AF: 0.298

Gnomad FIN exome AF: 0.363

Gnomad NFE exome AF: 0.362

Gnomad OTH exome AF: 0.341

GnomAD4 exome AF: 0.354 AC: 516547 AN: 1461082 Hom.: 94120 Cov.: 44 AF XY: 0.352 AC XY: 256077 AN XY: 726840

Gnomad4 AFR exome AF: 0.0765

Gnomad4 AMR exome AF: 0.380

Gnomad4 ASJ exome AF: 0.384

Gnomad4 EAS exome AF: 0.178

Gnomad4 SAS exome AF: 0.300

Gnomad4 FIN exome AF: 0.365

Gnomad4 NFE exome AF: 0.371

Gnomad4 OTH exome AF: 0.338

GnomAD4 genome AF: 0.281 AC: 42791 AN: 152052 Hom.: 7276 Cov.: 32 AF XY: 0.282 AC XY: 20963 AN XY: 74308

Gnomad4 AFR AF: 0.0889

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.301

Alfa AF: 0.334 Hom.: 11022

Bravo AF: 0.271

Asia WGS AF: 0.214 AC: 748 AN: 3478

EpiCase AF: 0.355

EpiControl AF: 0.357

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.13
DANN	Benign	0.82
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1566290; hg19: chr17-71239087; COSMIC: COSV52145567; COSMIC: COSV52145567;