rs10492813

Variant names:

• chr16-72088564-C-T
• rs10492813
• NM_017853.3:c.284+423G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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]

ENSG00000310525 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017853.3. 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
	TXNL4B	NM_017853.3	MANE Select	c.284+423G>A		intron	N/A	NP_060323.1
	TXNL4B	NM_001142317.2		c.284+423G>A		intron	N/A	NP_001135789.1
	TXNL4B	NM_001142318.2		c.284+423G>A		intron	N/A	NP_001135790.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TXNL4B	ENST00000268483.8	TSL:1 MANE Select	c.284+423G>A		intron	N/A	ENSP00000268483.3
	ENSG00000310525	ENST00000562153.6	TSL:4	n.284+423G>A		intron	N/A	ENSP00000454635.2
	TXNL4B	ENST00000423037.5	TSL:4	c.284+423G>A		intron	N/A	ENSP00000408130.1

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

African (AFR) AF: 0.741 AC: 30750 AN: 41500

American (AMR) AF: 0.379 AC: 5792 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1514 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1723 AN: 5174

South Asian (SAS) AF: 0.487 AC: 2346 AN: 4820

European-Finnish (FIN) AF: 0.382 AC: 4040 AN: 10568

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28509 AN: 67962

Other (OTH) AF: 0.500 AC: 1055 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.49
DANN	Benign	0.44
PhyloP100		-0.76
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: rs10492813; hg19: chr16-72122463;