16-72080103-C-T

Position:

• chr16-72080103-C-T

Variant summary

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

The ENST00000562153.5(TXNL4B):​c.284+8884G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,500 control chromosomes in the GnomAD database, including 3,310 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 0.20 (3310 hom., cov: 32)
• Consequence: TXNL4B ENST00000562153.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

TXNL4B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.72080103C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TXNL4B	ENST00000562153.5	c.284+8884G>A		intron_variant		4		ENSP00000454635.2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30644 AN: 151428 Hom.: 3304 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.202 AC: 30666 AN: 151500 Hom.: 3310 Cov.: 32 AF XY: 0.203 AC XY: 15002 AN XY: 73978

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.192

Alfa AF: 0.198 Hom.: 3169

Bravo AF: 0.212

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.5
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs217181; hg19: chr16-72114002;