chr6-158418122-C-G

Variant names:

• chr6-158418122-C-G
• rs609621
• NM_020245.5:c.381+4929C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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]

ENSG00000274023 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TULP4	NM_020245.5	c.381+4929C>G		intron_variant	Intron 2 of 13	ENST00000367097.8	NP_064630.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TULP4	ENST00000367097.8	c.381+4929C>G		intron_variant	Intron 2 of 13	1	NM_020245.5	ENSP00000356064.3
TULP4	ENST00000367094.6	c.381+4929C>G		intron_variant	Intron 2 of 12	1		ENSP00000356061.2
TULP4	ENST00000616856.1	n.953+4929C>G		intron_variant	Intron 2 of 7	2
ENSG00000274023	ENST00000619713.1	n.21-9717C>G		intron_variant	Intron 1 of 1	5

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

African (AFR) AF: 0.110 AC: 4107 AN: 37282

American (AMR) AF: 0.0153 AC: 211 AN: 13832

Ashkenazi Jewish (ASJ) AF: 0.0192 AC: 65 AN: 3382

East Asian (EAS) AF: 0.00 AC: 0 AN: 4812

South Asian (SAS) AF: 0.000226 AC: 1 AN: 4420

European-Finnish (FIN) AF: 0.00295 AC: 22 AN: 7462

Middle Eastern (MID) AF: 0.00719 AC: 2 AN: 278

European-Non Finnish (NFE) AF: 0.00332 AC: 214 AN: 64524

Other (OTH) AF: 0.0248 AC: 47 AN: 1892

Alfa AF: 0.00 Hom.: 0

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
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs609621; hg19: chr6-158839154;