rs262825

Variant names:

• chr6-158257599-A-G
• rs262825
• XM_011535946.2:c.-1967+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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000620026.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TULP4	ENST00000620026.1	TSL:4	n.68+25296A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs262825;

hg19: chr6-158678631;