NM_020784.3:c.*946T>C

Variant names:

• chr14-52431358-A-G
• rs1565970
• NM_020784.3:c.*946T>C

Variant summary

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

The NM_020784.3(TXNDC16):​c.*946T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0955 in 152,260 control chromosomes in the GnomAD database, including 813 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 0.096 (813 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: TXNDC16 NM_020784.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 11 publications found

Genes affected

TXNDC16 (HGNC:19965): (thioredoxin domain containing 16) Located in endoplasmic reticulum lumen. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020784.3. 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
	TXNDC16	NM_020784.3	MANE Select	c.*946T>C		3_prime_UTR	Exon 21 of 21	NP_065835.2	Q9P2K2
	TXNDC16	NM_001160047.2		c.*946T>C		3_prime_UTR	Exon 21 of 21	NP_001153519.1	B7ZME4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TXNDC16	ENST00000281741.9	TSL:1 MANE Select	c.*946T>C		3_prime_UTR	Exon 21 of 21	ENSP00000281741.4	Q9P2K2
	TXNDC16	ENST00000936707.1		c.*946T>C		3_prime_UTR	Exon 21 of 21	ENSP00000606766.1
	TXNDC16	ENST00000956219.1		c.*946T>C		3_prime_UTR	Exon 22 of 22	ENSP00000626278.1

Frequencies

GnomAD3 genomes AF: 0.0956 AC: 14546 AN: 152142 Hom.: 813 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0566

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.100

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0955 AC: 14543 AN: 152260 Hom.: 813 Cov.: 33 AF XY: 0.0946 AC XY: 7040 AN XY: 74452

African (AFR) AF: 0.135 AC: 5627 AN: 41548

American (AMR) AF: 0.121 AC: 1850 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3468

East Asian (EAS) AF: 0.176 AC: 913 AN: 5178

South Asian (SAS) AF: 0.0344 AC: 166 AN: 4822

European-Finnish (FIN) AF: 0.0566 AC: 601 AN: 10610

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0709 AC: 4819 AN: 68014

Other (OTH) AF: 0.0989 AC: 209 AN: 2114

Alfa AF: 0.0800 Hom.: 740

Bravo AF: 0.107

Asia WGS AF: 0.102 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		0.34
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: rs1565970; hg19: chr14-52898076;