rs585078

Variant names:

• chr6-158465959-A-G
• rs585078
• NM_020245.5:c.1026+4230A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020245.5(TULP4):​c.1026+4230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,078 control chromosomes in the GnomAD database, including 14,585 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 0.42 (14585 hom., cov: 32)
• Consequence: TULP4 NM_020245.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TULP4	NM_020245.5	c.1026+4230A>G		intron_variant	Intron 6 of 13	ENST00000367097.8	NP_064630.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TULP4	ENST00000367097.8	c.1026+4230A>G		intron_variant	Intron 6 of 13	1	NM_020245.5	ENSP00000356064.3
TULP4	ENST00000367094.6	c.1026+4230A>G		intron_variant	Intron 6 of 12	1		ENSP00000356061.2
TULP4	ENST00000613390.1	n.78+4230A>G		intron_variant	Intron 1 of 5	5		ENSP00000481804.1
TULP4	ENST00000616856.1	n.1598+4230A>G		intron_variant	Intron 6 of 7	2

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63455 AN: 151960 Hom.: 14551 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.418 AC: 63541 AN: 152078 Hom.: 14585 Cov.: 32 AF XY: 0.414 AC XY: 30799 AN XY: 74314

African (AFR) AF: 0.621 AC: 25747 AN: 41472

American (AMR) AF: 0.364 AC: 5567 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3466

East Asian (EAS) AF: 0.365 AC: 1888 AN: 5172

South Asian (SAS) AF: 0.518 AC: 2497 AN: 4818

European-Finnish (FIN) AF: 0.249 AC: 2637 AN: 10572

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22692 AN: 67986

Other (OTH) AF: 0.395 AC: 834 AN: 2114

Alfa AF: 0.399 Hom.: 1719

Bravo AF: 0.429

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.38
PhyloP100		-0.67
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs585078; hg19: chr6-158886991;