rs9456307

Variant names:

• chr6-158508410-T-A
• rs9456307
• NM_020245.5:c.*1716T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-158508410-T-A
• chr6-158508410-T-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.*1716T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0784 in 152,232 control chromosomes in the GnomAD database, including 638 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 0.078 (638 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TULP4 NM_020245.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615
• Publications: 32 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TULP4	NM_020245.5	MANE Select	c.*1716T>A		3_prime_UTR	Exon 14 of 14	NP_064630.2	Q9NRJ4-1
	TULP4	NM_001007466.3		c.*1810T>A		3_prime_UTR	Exon 13 of 13	NP_001007467.1	Q9NRJ4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TULP4	ENST00000367097.8	TSL:1 MANE Select	c.*1716T>A		3_prime_UTR	Exon 14 of 14	ENSP00000356064.3	Q9NRJ4-1
	TULP4	ENST00000367094.6	TSL:1	c.*1810T>A		downstream_gene	N/A	ENSP00000356061.2	Q9NRJ4-2

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11919 AN: 152114 Hom.: 634 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0657

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.0837

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0784 AC: 11937 AN: 152232 Hom.: 638 Cov.: 33 AF XY: 0.0771 AC XY: 5743 AN XY: 74444

African (AFR) AF: 0.147 AC: 6091 AN: 41482

American (AMR) AF: 0.0656 AC: 1004 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3470

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5192

South Asian (SAS) AF: 0.0835 AC: 403 AN: 4826

European-Finnish (FIN) AF: 0.0162 AC: 172 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0559 AC: 3801 AN: 68030

Other (OTH) AF: 0.0829 AC: 175 AN: 2112

Alfa AF: 0.0632 Hom.: 58

Bravo AF: 0.0843

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.68
PhyloP100		0.61
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9456307; hg19: chr6-158929442;