Variant rs2273001 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003322.6(TULP1):c.499+26C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 1,612,748 control chromosomes in the GnomAD database, including 389,180 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.65 ( 33011 hom., cov: 31)

Exomes 𝑓: 0.70 ( 356169 hom. )

Consequence

TULP1
NM_003322.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.879

Variant links:

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 links:

TULP1 (HGNC:):

TULP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 6-35510835-G-A is Benign according to our data. Variant chr6-35510835-G-A is described in ClinVar as [Benign]. Clinvar id is 1290548.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TULP1	NM_003322.6 linkuse as main transcript	c.499+26C>T		intron_variant		ENST00000229771.11	NP_003313.3	O00294-1Q0QD38
TULP1	NM_001289395.2 linkuse as main transcript	c.340+26C>T		intron_variant			NP_001276324.1	O00294-2F1T0I9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TULP1	ENST00000229771.11 linkuse as main transcript	c.499+26C>T		intron_variant		1	NM_003322.6	ENSP00000229771.6		O00294-1

Frequencies

GnomAD3 genomes

AF:

0.654

AC:

99398

AN:

151910

Hom.:

32994

Cov.:

show subpopulations

Gnomad AFR

AF:

0.525

Gnomad AMI

AF:

0.827

Gnomad AMR

AF:

0.653

Gnomad ASJ

AF:

0.727

Gnomad EAS

AF:

0.729

Gnomad SAS

AF:

0.692

Gnomad FIN

AF:

0.748

Gnomad MID

AF:

0.636

Gnomad NFE

AF:

0.705

Gnomad OTH

AF:

0.647

GnomAD3 exomes

AF:

0.689

AC:

172626

AN:

250402

Hom.:

59896

AF XY:

0.696

AC XY:

94271

AN XY:

135458

show subpopulations

Gnomad AFR exome

AF:

0.522

Gnomad AMR exome

AF:

0.657

Gnomad ASJ exome

AF:

0.713

Gnomad EAS exome

AF:

0.722

Gnomad SAS exome

AF:

0.703

Gnomad FIN exome

AF:

0.734

Gnomad NFE exome

AF:

0.703

Gnomad OTH exome

AF:

0.704

GnomAD4 exome

AF:

0.698

AC:

1018945

AN:

1460720

Hom.:

356169

Cov.:

AF XY:

0.698

AC XY:

507540

AN XY:

726720

show subpopulations

Gnomad4 AFR exome

AF:

0.525

Gnomad4 AMR exome

AF:

0.654

Gnomad4 ASJ exome

AF:

0.719

Gnomad4 EAS exome

AF:

0.729

Gnomad4 SAS exome

AF:

0.705

Gnomad4 FIN exome

AF:

0.738

Gnomad4 NFE exome

AF:

0.701

Gnomad4 OTH exome

AF:

0.689

GnomAD4 genome

AF:

0.654

AC:

99452

AN:

152028

Hom.:

33011

Cov.:

AF XY:

0.659

AC XY:

48949

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.525

Gnomad4 AMR

AF:

0.653

Gnomad4 ASJ

AF:

0.727

Gnomad4 EAS

AF:

0.730

Gnomad4 SAS

AF:

0.693

Gnomad4 FIN

AF:

0.748

Gnomad4 NFE

AF:

0.705

Gnomad4 OTH

AF:

0.648

Alfa

AF:

0.682

Hom.:

6408

Bravo

AF:

0.642

Asia WGS

AF:

0.706

AC:

2454

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Retinitis pigmentosa 14

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Leber congenital amaurosis 15

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.5

DANN

Benign

0.59

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over