chr11-33067608-A-G

Position:

• chr11-33067608-A-G

Variant summary

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

The ENST00000334274.9(TCP11L1):​c.1155-1079A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,108 control chromosomes in the GnomAD database, including 6,742 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 0.29 (6742 hom., cov: 32)
• Consequence: TCP11L1 ENST00000334274.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

Genes affected

TCP11L1 (HGNC:25655): (t-complex 11 like 1) Predicted to be involved in signal transduction. Located in microtubule. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCP11L1	NM_018393.4	c.1155-1079A>G		intron_variant		ENST00000334274.9	NP_060863.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCP11L1	ENST00000334274.9	c.1155-1079A>G		intron_variant		1	NM_018393.4	ENSP00000335595	P1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43366 AN: 151988 Hom.: 6750 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.285 AC: 43363 AN: 152108 Hom.: 6742 Cov.: 32 AF XY: 0.289 AC XY: 21501 AN XY: 74344

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.297

Alfa AF: 0.285 Hom.: 775

Bravo AF: 0.268

Asia WGS AF: 0.393 AC: 1364 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	1.2
DANN	Benign	0.48

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: rs752744; hg19: chr11-33089154;