rs10492813

chr16-72088564-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017853.3(TXNL4B):c.284+423G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,098 control chromosomes in the GnomAD database, including 20,958 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 0.50 (20958 hom., cov: 33)
• Consequence: TXNL4B NM_017853.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755

Genes affected

TXNL4B (HGNC:26041): (thioredoxin like 4B) Predicted to be involved in mRNA splicing, via spliceosome. Located in cytosol and nucleoplasm. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TXNL4B	NM_017853.3	c.284+423G>A		intron_variant		ENST00000268483.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TXNL4B	ENST00000268483.8	c.284+423G>A		intron_variant		1	NM_017853.3	P1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76074 AN: 151980 Hom.: 20921 Cov.: 33

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.501 AC: 76157 AN: 152098 Hom.: 20958 Cov.: 33 AF XY: 0.495 AC XY: 36818 AN XY: 74354

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.500

Alfa AF: 0.449 Hom.: 2774

Bravo AF: 0.505

Asia WGS AF: 0.438 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.49
Dann	Benign	0.44

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: rs10492813; hg19: chr16-72122463;