rs6920842

Variant names:

• chr6-158449515-G-C
• rs6920842
• NM_020245.5:c.724+339G>C

Variant summary

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

The NM_020245.5(TULP4):​c.724+339G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.097 in 151,884 control chromosomes in the GnomAD database, including 761 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 0.097 (761 hom., cov: 32)
• Consequence: TULP4 NM_020245.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 3 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=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020245.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TULP4	NM_020245.5	MANE Select	c.724+339G>C		intron	N/A	NP_064630.2
	TULP4	NM_001007466.3		c.724+339G>C		intron	N/A	NP_001007467.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TULP4	ENST00000367097.8	TSL:1 MANE Select	c.724+339G>C		intron	N/A	ENSP00000356064.3
	TULP4	ENST00000367094.6	TSL:1	c.724+339G>C		intron	N/A	ENSP00000356061.2
	TULP4	ENST00000616856.1	TSL:2	n.1296+339G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0971 AC: 14731 AN: 151766 Hom.: 762 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.0632

Gnomad EAS AF: 0.0725

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0865

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.0970 AC: 14731 AN: 151884 Hom.: 761 Cov.: 32 AF XY: 0.0976 AC XY: 7243 AN XY: 74234

African (AFR) AF: 0.128 AC: 5295 AN: 41498

American (AMR) AF: 0.0605 AC: 925 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0632 AC: 219 AN: 3464

East Asian (EAS) AF: 0.0725 AC: 355 AN: 4898

South Asian (SAS) AF: 0.0712 AC: 342 AN: 4802

European-Finnish (FIN) AF: 0.131 AC: 1393 AN: 10596

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0865 AC: 5882 AN: 68024

Other (OTH) AF: 0.0822 AC: 174 AN: 2116

Alfa AF: 0.0876 Hom.: 83

Bravo AF: 0.0923

Asia WGS AF: 0.0660 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		1.5
Mutation Taster		=99/1	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: rs6920842; hg19: chr6-158870547;