rs752744

Variant names:

• chr11-33067608-A-G
• rs752744
• NM_018393.4:c.1155-1079A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-33067608-A-G
• chr11-33067608-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018393.4(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 NM_018393.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TCP11L1	NM_018393.4	c.1155-1079A>G		intron_variant	Intron 8 of 9	ENST00000334274.9	NP_060863.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCP11L1	ENST00000334274.9	c.1155-1079A>G		intron_variant	Intron 8 of 9	1	NM_018393.4	ENSP00000335595.4

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

African (AFR) AF: 0.161 AC: 6699 AN: 41534

American (AMR) AF: 0.255 AC: 3898 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2129 AN: 5136

South Asian (SAS) AF: 0.371 AC: 1790 AN: 4826

European-Finnish (FIN) AF: 0.401 AC: 4242 AN: 10570

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22367 AN: 67978

Other (OTH) AF: 0.297 AC: 626 AN: 2110

Alfa AF: 0.280 Hom.: 785

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
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs752744; hg19: chr11-33089154;