rs745080

Variant names:

• chr14-52522510-G-A
• rs745080
• NM_020784.3:c.393-3217C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-52522510-G-A
• chr14-52522510-G-C
• chr14-52522510-G-T

Variant summary

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

The NM_020784.3(TXNDC16):​c.393-3217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,964 control chromosomes in the GnomAD database, including 9,848 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 0.36 (9848 hom., cov: 32)
• Consequence: TXNDC16 NM_020784.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TXNDC16	NM_020784.3	MANE Select	c.393-3217C>T		intron	N/A	NP_065835.2
	TXNDC16	NM_001160047.2		c.393-3232C>T		intron	N/A	NP_001153519.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TXNDC16	ENST00000281741.9	TSL:1 MANE Select	c.393-3217C>T		intron	N/A	ENSP00000281741.4
	TXNDC16	ENST00000557374.1	TSL:4	c.-295+29806C>T		intron	N/A	ENSP00000450839.1
	TXNDC16	ENST00000554399.1	TSL:4	n.207+29806C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54268 AN: 151846 Hom.: 9829 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.335

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.357 AC: 54320 AN: 151964 Hom.: 9848 Cov.: 32 AF XY: 0.362 AC XY: 26885 AN XY: 74294

African (AFR) AF: 0.356 AC: 14731 AN: 41424

American (AMR) AF: 0.316 AC: 4827 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2700 AN: 5170

South Asian (SAS) AF: 0.510 AC: 2454 AN: 4814

European-Finnish (FIN) AF: 0.396 AC: 4181 AN: 10558

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23289 AN: 67952

Other (OTH) AF: 0.334 AC: 705 AN: 2108

Alfa AF: 0.343 Hom.: 30545

Bravo AF: 0.348

Asia WGS AF: 0.530 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.53
PhyloP100		0.29
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: rs745080; hg19: chr14-52989228;