rs745080

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

TXNDC16 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TXNDC16	NM_020784.3	c.393-3217C>T		intron_variant		ENST00000281741.9	NP_065835.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TXNDC16	ENST00000281741.9	c.393-3217C>T		intron_variant		1	NM_020784.3	ENSP00000281741.4
TXNDC16	ENST00000557374.1	c.-295+29806C>T		intron_variant		4		ENSP00000450839.1
TXNDC16	ENST00000554399.1	n.207+29806C>T		intron_variant		4

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

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.334

Alfa AF: 0.340 Hom.: 19653

Bravo AF: 0.348

Asia WGS AF: 0.530 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.53

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: rs745080; hg19: chr14-52989228;