rs781381

Positions:

• chr14-52444075-A-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

TXNDC16 (HGNC:19965): (thioredoxin domain containing 16) Located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TXNDC16	NM_020784.3	c.1843-3351T>G		intron_variant		ENST00000281741.9	NP_065835.2
TXNDC16	NM_001160047.2	c.1828-3351T>G		intron_variant			NP_001153519.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TXNDC16	ENST00000281741.9	c.1843-3351T>G		intron_variant		1	NM_020784.3	ENSP00000281741	P1
TXNDC16	ENST00000554399.1	n.208-3351T>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0669

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.0357

Gnomad4 FIN AF: 0.0568

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0804 Hom.: 69

Bravo AF: 0.121

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs781381; hg19: chr14-52910793;