16-72077611-C-T

Variant names:

• chr16-72077611-C-T
• rs382695
• ENST00000562153.5:c.284+11376G>A

Variant summary

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

The ENST00000562153.5(TXNL4B):​c.284+11376G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 152,108 control chromosomes in the GnomAD database, including 671 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 0.073 (671 hom., cov: 29)
• Consequence: TXNL4B ENST00000562153.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TXNL4B	ENST00000562153.5	c.284+11376G>A		intron_variant	Intron 3 of 3	4		ENSP00000454635.2

Frequencies

GnomAD3 genomes AF: 0.0725 AC: 11025 AN: 151990 Hom.: 666 Cov.: 29

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.0490

Gnomad SAS AF: 0.0278

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0365

Gnomad OTH AF: 0.0637

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

GnomAD4 genome AF: 0.0727 AC: 11057 AN: 152108 Hom.: 671 Cov.: 29 AF XY: 0.0715 AC XY: 5316 AN XY: 74362

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0434

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.0280

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0365

Gnomad4 OTH AF: 0.0635

Alfa AF: 0.0566 Hom.: 51

Bravo AF: 0.0773

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs382695; hg19: chr16-72111510;