6-158259535-C-T

Variant names:

• chr6-158259535-C-T
• rs262826
• ENST00000620026.1:n.68+27232C>T

Variant summary

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

The ENST00000620026.1(TULP4):​n.68+27232C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,898 control chromosomes in the GnomAD database, including 16,317 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 0.46 (16317 hom., cov: 32)
• Consequence: TULP4 ENST00000620026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TULP4	XM_011535946.2	c.-1967+27232C>T		intron_variant	Intron 1 of 15		XP_011534248.1
TULP4	XM_047419079.1	c.-2082-22728C>T		intron_variant	Intron 1 of 16		XP_047275035.1
TULP4	XM_047419081.1	c.-2121-7699C>T		intron_variant	Intron 1 of 17		XP_047275037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TULP4	ENST00000620026.1	n.68+27232C>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69636 AN: 151780 Hom.: 16298 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.459 AC: 69695 AN: 151898 Hom.: 16317 Cov.: 32 AF XY: 0.461 AC XY: 34241 AN XY: 74196

African (AFR) AF: 0.366 AC: 15165 AN: 41436

American (AMR) AF: 0.524 AC: 8008 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1547 AN: 3458

East Asian (EAS) AF: 0.537 AC: 2773 AN: 5160

South Asian (SAS) AF: 0.403 AC: 1940 AN: 4816

European-Finnish (FIN) AF: 0.552 AC: 5806 AN: 10516

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32895 AN: 67920

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.347 Hom.: 948

Bravo AF: 0.459

Asia WGS AF: 0.453 AC: 1575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs262826; hg19: chr6-158680567;