rs262825

Variant names:

• chr6-158257599-A-G
• rs262825
• ENST00000620026.1:n.68+25296A>G

Variant summary

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

The ENST00000620026.1(TULP4):​n.68+25296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,900 control chromosomes in the GnomAD database, including 16,389 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 (16389 hom., cov: 32)
• Consequence: TULP4 ENST00000620026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 8 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=-0.99).
• 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+25296A>G		intron_variant	Intron 1 of 15		XP_011534248.1
TULP4	XM_047419079.1	c.-2082-24664A>G		intron_variant	Intron 1 of 16		XP_047275035.1
TULP4	XM_047419081.1	c.-2121-9635A>G		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+25296A>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69753 AN: 151782 Hom.: 16370 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.460 AC: 69814 AN: 151900 Hom.: 16389 Cov.: 32 AF XY: 0.463 AC XY: 34332 AN XY: 74224

African (AFR) AF: 0.367 AC: 15170 AN: 41382

American (AMR) AF: 0.525 AC: 8019 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2777 AN: 5166

South Asian (SAS) AF: 0.403 AC: 1940 AN: 4812

European-Finnish (FIN) AF: 0.554 AC: 5844 AN: 10542

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

European-Non Finnish (NFE) AF: 0.485 AC: 32948 AN: 67936

Other (OTH) AF: 0.458 AC: 967 AN: 2112

Alfa AF: 0.474 Hom.: 12287

Bravo AF: 0.459

Asia WGS AF: 0.454 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.33
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs262825; hg19: chr6-158678631;