6-35500882-A-G

Position:

• chr6-35500882-A-G

Variant summary

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

The NM_003322.6(TULP1):​c.1324-730T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,224 control chromosomes in the GnomAD database, including 2,124 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 0.16 (2124 hom., cov: 32)
• Consequence: TULP1 NM_003322.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

Genes affected

TULP1 (HGNC:12423): (TUB like protein 1) This gene encodes a member of the tubby-like gene family (TULPs). Members of this family have been identified in plants, vertebrates, and invertebrates. TULP proteins share a conserved C-terminal region of approximately 200 amino acid residues. The protein encoded by this gene is thought to play a role in the physiology of photoreceptors. Mutations in this gene are associated with recessive juvenile retinitis pigmentosa and Leber congenital amaurosis-15. [provided by RefSeq, Nov 2016]

TULP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TULP1	NM_003322.6	c.1324-730T>C		intron_variant		ENST00000229771.11	NP_003313.3
TULP1	NM_001289395.2	c.1165-730T>C		intron_variant			NP_001276324.1
LOC124901309	XR_007059561.1	n.75+2675A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TULP1	ENST00000229771.11	c.1324-730T>C		intron_variant		1	NM_003322.6	ENSP00000229771.6
TULP1	ENST00000322263.8	c.1165-730T>C		intron_variant		1		ENSP00000319414.4
TULP1	ENST00000614066.4	c.1318-730T>C		intron_variant		5		ENSP00000477534.1
TULP1	ENST00000495781.1	n.500-730T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24108 AN: 152104 Hom.: 2107 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0999

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.159 AC: 24164 AN: 152224 Hom.: 2124 Cov.: 32 AF XY: 0.155 AC XY: 11536 AN XY: 74438

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.0999

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0704

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.148

Alfa AF: 0.138 Hom.: 3024

Bravo AF: 0.174

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.88

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: rs1883636; hg19: chr6-35468659;