chr6-158464726-T-C

Position:

• chr6-158464726-T-C

Variant summary

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

The NM_020245.5(TULP4):​c.1026+2997T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,054 control chromosomes in the GnomAD database, including 14,581 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 0.42 (14581 hom., cov: 32)
• Consequence: TULP4 NM_020245.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TULP4	NM_020245.5	c.1026+2997T>C		intron_variant		ENST00000367097.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TULP4	ENST00000367097.8	c.1026+2997T>C		intron_variant		1	NM_020245.5	P1
TULP4	ENST00000367094.6	c.1026+2997T>C		intron_variant		1
TULP4	ENST00000613390.1	c.80+2997T>C		intron_variant, NMD_transcript_variant		5
TULP4	ENST00000616856.1	n.1598+2997T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63459 AN: 151936 Hom.: 14547 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.418 AC: 63545 AN: 152054 Hom.: 14581 Cov.: 32 AF XY: 0.414 AC XY: 30812 AN XY: 74338

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.394

Alfa AF: 0.389 Hom.: 1566

Bravo AF: 0.429

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.75

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: rs651333; hg19: chr6-158885758;