chr6-158508410-T-A

Position:

• chr6-158508410-T-A

Variant summary

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

The NM_020245.5(TULP4):​c.*1716T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0784 in 152,232 control chromosomes in the GnomAD database, including 638 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 0.078 (638 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TULP4 NM_020245.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615

Genes affected

TULP4 (HGNC:15530): (TUB like protein 4) Predicted to be involved in protein ubiquitination. Located in cytoplasm. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TULP4	NM_020245.5	c.*1716T>A		3_prime_UTR_variant	14/14	ENST00000367097.8	NP_064630.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TULP4	ENST00000367097.8	c.*1716T>A		3_prime_UTR_variant	14/14	1	NM_020245.5	ENSP00000356064.3
TULP4	ENST00000367094.6	c.*1810T>A		downstream_gene_variant		1		ENSP00000356061.2

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11919 AN: 152114 Hom.: 634 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0657

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.0837

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.0784 AC: 11937 AN: 152232 Hom.: 638 Cov.: 33 AF XY: 0.0771 AC XY: 5743 AN XY: 74444

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.0656

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0835

Gnomad4 FIN AF: 0.0162

Gnomad4 NFE AF: 0.0559

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0632 Hom.: 58

Bravo AF: 0.0843

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.68
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9456307; hg19: chr6-158929442;