rs705936

Positions:

• chr6-158391329-A-G
• chr6-158391329-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.253-21736A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 152,214 control chromosomes in the GnomAD database, including 62,570 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 0.91 (62570 hom., cov: 31)
• Consequence: TULP4 NM_020245.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

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]

TULP4 (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 (AMR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TULP4	NM_020245.5	c.253-21736A>G		intron_variant		ENST00000367097.8	NP_064630.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TULP4	ENST00000367097.8	c.253-21736A>G		intron_variant		1	NM_020245.5	ENSP00000356064.3
TULP4	ENST00000367094.6	c.253-21736A>G		intron_variant		1		ENSP00000356061.2
TULP4	ENST00000616856.1	n.825-21736A>G		intron_variant		2
ENSG00000274023	ENST00000619713.1	n.21-36510A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137830 AN: 152096 Hom.: 62505 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.906 AC: 137953 AN: 152214 Hom.: 62570 Cov.: 31 AF XY: 0.906 AC XY: 67467 AN XY: 74426

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.941

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.918

Alfa AF: 0.918 Hom.: 62866

Bravo AF: 0.907

Asia WGS AF: 0.926 AC: 3222 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	3.4
DANN	Benign	0.68

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: rs705936; hg19: chr6-158812361;