rs609621

chr6-158418122-C-Gchr6-158418122-C-T

Variant summary

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

The NM_020245.5(TULP4):c.381+4929C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 138,746 control chromosomes in the GnomAD database, including 236 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 0.034 (236 hom., cov: 24)
• Consequence: TULP4 NM_020245.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TULP4	NM_020245.5	c.381+4929C>G		intron_variant		ENST00000367097.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TULP4	ENST00000367097.8	c.381+4929C>G		intron_variant		1	NM_020245.5	P1
TULP4	ENST00000367094.6	c.381+4929C>G		intron_variant		1
	ENST00000619713.1	n.21-9717C>G		intron_variant, non_coding_transcript_variant		5
TULP4	ENST00000616856.1	n.953+4929C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0335 AC: 4646 AN: 138702 Hom.: 230 Cov.: 24

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.00232

Gnomad AMR AF: 0.0153

Gnomad ASJ AF: 0.0192

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000450

Gnomad FIN AF: 0.00295

Gnomad MID AF: 0.0132

Gnomad NFE AF: 0.00332

Gnomad OTH AF: 0.0251

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

GnomAD4 genome AF: 0.0337 AC: 4671 AN: 138746 Hom.: 236 Cov.: 24 AF XY: 0.0335 AC XY: 2229 AN XY: 66614

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0153

Gnomad4 ASJ AF: 0.0192

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000226

Gnomad4 FIN AF: 0.00295

Gnomad4 NFE AF: 0.00332

Gnomad4 OTH AF: 0.0248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.10
Dann	Benign	0.32

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

Publications

LitVar

Other links and lift over

dbSNP: rs609621; hg19: chr6-158839154;