1-117624128-A-G

Variant names:

• chr1-117624128-A-G
• rs2066411
• NM_017709.4:c.*84A>G

Variant summary

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

The NM_017709.4(TENT5C):​c.*84A>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 0.231 in 1,159,988 control chromosomes in the GnomAD database, including 31,647 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 0.24 (4086 hom., cov: 29)
  • Exomes 𝑓: 0.23 (27561 hom.)
• Consequence: TENT5C NM_017709.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16
• Publications: 10 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENT5C	NM_017709.4	c.*84A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000369448.4	NP_060179.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT5C	ENST00000369448.4	c.*84A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_017709.4	ENSP00000358458.3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 34981 AN: 147724 Hom.: 4083 Cov.: 29

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.268

GnomAD4 exome AF: 0.230 AC: 233007 AN: 1012222 Hom.: 27561 Cov.: 14 AF XY: 0.233 AC XY: 116822 AN XY: 501054

African (AFR) AF: 0.196 AC: 4356 AN: 22216

American (AMR) AF: 0.321 AC: 6359 AN: 19798

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 5129 AN: 17172

East Asian (EAS) AF: 0.206 AC: 6919 AN: 33516

South Asian (SAS) AF: 0.308 AC: 17219 AN: 55936

European-Finnish (FIN) AF: 0.220 AC: 10115 AN: 45938

Middle Eastern (MID) AF: 0.309 AC: 1227 AN: 3968

European-Non Finnish (NFE) AF: 0.222 AC: 170809 AN: 769550

Other (OTH) AF: 0.246 AC: 10874 AN: 44128

GnomAD4 genome AF: 0.237 AC: 34992 AN: 147766 Hom.: 4086 Cov.: 29 AF XY: 0.244 AC XY: 17486 AN XY: 71712

African (AFR) AF: 0.205 AC: 8136 AN: 39640

American (AMR) AF: 0.320 AC: 4796 AN: 14984

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1053 AN: 3442

East Asian (EAS) AF: 0.223 AC: 1116 AN: 4994

South Asian (SAS) AF: 0.281 AC: 1324 AN: 4704

European-Finnish (FIN) AF: 0.243 AC: 2316 AN: 9516

Middle Eastern (MID) AF: 0.281 AC: 77 AN: 274

European-Non Finnish (NFE) AF: 0.229 AC: 15403 AN: 67264

Other (OTH) AF: 0.267 AC: 547 AN: 2048

Alfa AF: 0.229 Hom.: 6006

Bravo AF: 0.236

Asia WGS AF: 0.247 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	14
DANN	Benign	0.87
PhyloP100		2.2
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: rs2066411; hg19: chr1-118166750; COSMIC: COSV65616308;