1-117623069-C-T

Variant names:

• chr1-117623069-C-T
• rs1630312
• NM_017709.4:c.201C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_017709.4(TENT5C):​c.201C>T​(p.His67His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,613,976 control chromosomes in the GnomAD database, including 71,316 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 0.27 (5896 hom., cov: 32)
  • Exomes 𝑓: 0.29 (65420 hom.)
• Consequence: TENT5C NM_017709.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 27 publications found

Genes affected

TENT5C (HGNC:24712): (terminal nucleotidyltransferase 5C) Enables RNA adenylyltransferase activity. Involved in mRNA stabilization. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BP7: Synonymous conserved (PhyloP=0.434 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017709.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENT5C	NM_017709.4	MANE Select	c.201C>T	p.His67His	synonymous	Exon 2 of 2	NP_060179.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENT5C	ENST00000369448.4	TSL:1 MANE Select	c.201C>T	p.His67His	synonymous	Exon 2 of 2	ENSP00000358458.3	Q5VWP2
	TENT5C	ENST00000880490.1		c.201C>T	p.His67His	synonymous	Exon 3 of 3	ENSP00000550549.1
	TENT5C	ENST00000880491.1		c.201C>T	p.His67His	synonymous	Exon 2 of 2	ENSP00000550550.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40893 AN: 151980 Hom.: 5893 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.268

GnomAD2 exomes AF: 0.260 AC: 65414 AN: 251420 AF XY: 0.262

Gnomad AFR exome AF: 0.219

Gnomad AMR exome AF: 0.204

Gnomad ASJ exome AF: 0.210

Gnomad EAS exome AF: 0.0932

Gnomad FIN exome AF: 0.357

Gnomad NFE exome AF: 0.311

Gnomad OTH exome AF: 0.259

GnomAD4 exome AF: 0.295 AC: 430850 AN: 1461878 Hom.: 65420 Cov.: 65 AF XY: 0.292 AC XY: 212585 AN XY: 727236

African (AFR) AF: 0.215 AC: 7188 AN: 33480

American (AMR) AF: 0.210 AC: 9379 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 5441 AN: 26136

East Asian (EAS) AF: 0.144 AC: 5735 AN: 39700

South Asian (SAS) AF: 0.203 AC: 17508 AN: 86258

European-Finnish (FIN) AF: 0.362 AC: 19316 AN: 53420

Middle Eastern (MID) AF: 0.212 AC: 1222 AN: 5768

European-Non Finnish (NFE) AF: 0.314 AC: 348715 AN: 1111998

Other (OTH) AF: 0.271 AC: 16346 AN: 60396

GnomAD4 genome AF: 0.269 AC: 40904 AN: 152098 Hom.: 5896 Cov.: 32 AF XY: 0.266 AC XY: 19798 AN XY: 74348

African (AFR) AF: 0.219 AC: 9089 AN: 41462

American (AMR) AF: 0.260 AC: 3976 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 748 AN: 3472

East Asian (EAS) AF: 0.105 AC: 541 AN: 5176

South Asian (SAS) AF: 0.210 AC: 1014 AN: 4824

European-Finnish (FIN) AF: 0.351 AC: 3707 AN: 10568

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21102 AN: 67982

Other (OTH) AF: 0.266 AC: 562 AN: 2114

Alfa AF: 0.259 Hom.: 2339

EpiCase AF: 0.304

EpiControl AF: 0.293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	11
DANN	Benign	0.82
PhyloP100		0.43
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: rs1630312; hg19: chr1-118165691; COSMIC: COSV65616400;