rs781381

Variant names:

• chr14-52444075-A-C
• rs781381
• NM_020784.3:c.1843-3351T>G

Variant summary

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

The NM_020784.3(TXNDC16):​c.1843-3351T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,146 control chromosomes in the GnomAD database, including 1,002 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 0.10 (1002 hom., cov: 32)
• Consequence: TXNDC16 NM_020784.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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.1843-3351T>G		intron	N/A	NP_065835.2
	TXNDC16	NM_001160047.2		c.1828-3351T>G		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.1843-3351T>G		intron	N/A	ENSP00000281741.4
	TXNDC16	ENST00000554399.1	TSL:4	n.208-3351T>G		intron	N/A
	TXNDC16	ENST00000555312.2	TSL:5	n.*361-3351T>G		intron	N/A	ENSP00000451619.2

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15952 AN: 152026 Hom.: 1002 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.105 AC: 15949 AN: 152146 Hom.: 1002 Cov.: 32 AF XY: 0.104 AC XY: 7755 AN XY: 74386

African (AFR) AF: 0.151 AC: 6282 AN: 41496

American (AMR) AF: 0.163 AC: 2495 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0669 AC: 232 AN: 3470

East Asian (EAS) AF: 0.186 AC: 959 AN: 5166

South Asian (SAS) AF: 0.0357 AC: 172 AN: 4822

European-Finnish (FIN) AF: 0.0568 AC: 603 AN: 10610

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0713 AC: 4847 AN: 67980

Other (OTH) AF: 0.109 AC: 231 AN: 2110

Alfa AF: 0.0830 Hom.: 78

Bravo AF: 0.121

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.76
PhyloP100		1.4
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: rs781381; hg19: chr14-52910793;