16-72077611-C-T

Position:

• chr16-72077611-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+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:):

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/exons	MANE	Protein	UniProt
		n.72077611C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TXNL4B	ENST00000562153.5	c.284+11376G>A		intron_variant		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;