rs262825

Positions:

• chr6-158257599-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011535946.2(TULP4):​c.-1967+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 XM_011535946.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TULP4	XM_011535946.2	c.-1967+25296A>G		intron_variant			XP_011534248.1
TULP4	XM_017011070.2	c.-1967+25296A>G		intron_variant			XP_016866559.1
TULP4	XM_047419079.1	c.-2082-24664A>G		intron_variant			XP_047275035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TULP4	ENST00000620026.1	n.68+25296A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.458

Alfa AF: 0.472 Hom.: 8907

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs262825; hg19: chr6-158678631;