rs9355652

chr6-158360403-A-Gchr6-158360403-A-T

Variant summary

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

The NM_020245.5(TULP4):c.252+46135A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,118 control chromosomes in the GnomAD database, including 2,464 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 0.15 (2464 hom., cov: 31)
• Consequence: TULP4 NM_020245.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TULP4	NM_020245.5	c.252+46135A>G		intron_variant		ENST00000367097.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TULP4	ENST00000367097.8	c.252+46135A>G		intron_variant		1	NM_020245.5	P1
TULP4	ENST00000367094.6	c.252+46135A>G		intron_variant		1
	ENST00000619713.1	n.21-67436A>G		intron_variant, non_coding_transcript_variant		5
TULP4	ENST00000616856.1	n.824+46135A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22986 AN: 152000 Hom.: 2457 Cov.: 31

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.151 AC: 23012 AN: 152118 Hom.: 2464 Cov.: 31 AF XY: 0.158 AC XY: 11730 AN XY: 74338

Gnomad4 AFR AF: 0.0521

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.165

Alfa AF: 0.149 Hom.: 883

Bravo AF: 0.162

Asia WGS AF: 0.291 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.33

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

Publications

LitVar

Other links and lift over

dbSNP: rs9355652; hg19: chr6-158781435;