chr6-158465826-C-T

Variant names:

• chr6-158465826-C-T
• rs635995
• NM_020245.5:c.1026+4097C>T

Variant summary

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

The NM_020245.5(TULP4):​c.1026+4097C>T 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 151,980 control chromosomes in the GnomAD database, including 14,586 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 (14586 hom., cov: 33)
• Consequence: TULP4 NM_020245.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TULP4	NM_020245.5	c.1026+4097C>T		intron_variant	Intron 6 of 13	ENST00000367097.8	NP_064630.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TULP4	ENST00000367097.8	c.1026+4097C>T		intron_variant	Intron 6 of 13	1	NM_020245.5	ENSP00000356064.3
TULP4	ENST00000367094.6	c.1026+4097C>T		intron_variant	Intron 6 of 12	1		ENSP00000356061.2
TULP4	ENST00000613390.1	n.78+4097C>T		intron_variant	Intron 1 of 5	5		ENSP00000481804.1
TULP4	ENST00000616856.1	n.1598+4097C>T		intron_variant	Intron 6 of 7	2

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63440 AN: 151862 Hom.: 14552 Cov.: 33

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.418 AC: 63526 AN: 151980 Hom.: 14586 Cov.: 33 AF XY: 0.415 AC XY: 30801 AN XY: 74278

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.394

Alfa AF: 0.369 Hom.: 5005

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	-0.83
CADD	Benign	2.5
DANN	Benign	0.40

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: rs635995; hg19: chr6-158886858;